| Back to Long Tests report for BioC 3.20 |
This page was generated on 2024-11-02 23:55 -0400 (Sat, 02 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4505 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 27/32 | Hostname | OS / Arch | CHECK | |||||||
| MungeSumstats 1.14.1 (landing page) Alan Murphy
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | |||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ||||||||
|
To the developers/maintainers of the MungeSumstats package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: MungeSumstats |
| Version: 1.14.1 |
| Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no MungeSumstats_1.14.1.tar.gz |
| StartedAt: 2024-11-02 16:34:32 -0400 (Sat, 02 Nov 2024) |
| EndedAt: 2024-11-02 16:44:06 -0400 (Sat, 02 Nov 2024) |
| EllapsedTime: 574.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MungeSumstats.Rcheck |
| Warnings: 0 |
MungeSumstats.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(MungeSumstats)
>
> test_check("MungeSumstats")
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c586e635f2e.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c581fd87224
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A0 A1 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A0 A1 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c586e635f2e.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.062 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c584b2b644f.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c581fd87224
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c584b2b644f.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.04 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Sorting coordinates with "data.table".
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c587936634a.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z
Found 1 Indels. These will be removed from the sumstats.
WARNING If you want to keep Indels, set the drop_indel param to FALSE & rerun MungeSumstats::format_sumstats()
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z/indel.tsv.gz
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Sorting coordinates with "data.table".
Filtering SNPs based on INFO score.
46 SNPs are below the INFO threshold of 0.9 and will be removed.
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z/info_filter.tsv.gz
INFO_filter==0. Skipping INFO score filtering step.
Filtering SNPs based on INFO score.
All rows have INFO>=0.9
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Sorting coordinates with "data.table".
3 p-values are >1 which LDSC/MAGMA may not be able to handle. These will be converted to 1.
5 p-values are <0 which LDSC/MAGMA may not be able to handle. These will be converted to 0.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Sorting coordinates with "data.table".
8 p-values are <=5e-324 which LDSC/MAGMA may not be able to handle. These will be converted to 0.
Reading header.
Tabular format detected.
Reading header.
Tabular format detected.
Reading header.
Tabular format detected.
Reading header.
VCF format detected.This will be converted to a standardised table format.
Importing tabular file: F:/biocbuild/bbs-3.20-bioc-longtests/meat/MungeSumstats.Rcheck/MungeSumstats/extdata/eduAttainOkbay.txt
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Computing Z-score from P using formula: `sign(BETA)*sqrt(stats::qchisq(P,1,lower=FALSE)`
Standardising column headers.
First line of summary statistics file:
SNP CHR BP A1 A2 FRQ BETA SE P Z newZ
Computing Z-score from BETA ans SE using formula: `BETA/SE`
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c585aa26c04.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5856107171
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName EAF Beta SE Pval CHR_BP_A2_A1
Standardising column headers.
First line of summary statistics file:
MarkerName EAF Beta SE Pval CHR_BP_A2_A1
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Column CHR_BP_A2_A1 has been separated into the columns CHR, BP, A2, A1
If this is the incorrect format for the column, update the column name to the correct format e.g.`CHR:BP:A2:A1` and format_sumstats().
Standardising column headers.
First line of summary statistics file:
SNP FRQ BETA SE P CHR BP A2 A1
Checking for incorrect base-pair positions
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c585aa26c04.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.076 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c585d5fe6b.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5856107171
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c585d5fe6b.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.04 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c586a957da0.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c588ab7ffa
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName EAF Beta SE Pval CHR_BP_A2_A1
Standardising column headers.
First line of summary statistics file:
MarkerName EAF Beta SE Pval CHR_BP_A2_A1
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Column CHR_BP_A2_A1 has been separated into the columns CHR, BP, A2, A1
If this is the incorrect format for the column, update the column name to the correct format e.g.`CHR:BP:A2:A1` and format_sumstats().
Standardising column headers.
First line of summary statistics file:
SNP FRQ BETA SE P CHR BP A2 A1
Checking for incorrect base-pair positions
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c586a957da0.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.074 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c585c35fa7.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c588ab7ffa
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c585c35fa7.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58bbc31b8.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c581f746e1
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS EAF Beta SE Pval alleles allele
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS EAF Beta SE Pval alleles allele
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Warning: Multiple columns in the sumstats file seem to relate to alleles A1>A2.
The column ALLELES will be kept whereas the column(s) ALLELE will be removed.
If this is not the correct column to keep, please remove all incorrect columns from those listed here before
running `format_sumstats()`.
Column ALLELES has been separated into the columns A1, A2
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58bbc31b8.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.038 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5862229d2.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c581f746e1
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5862229d2.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5864e24bf6.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c587e6f5053
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName A1 A2 EAF Beta SE Pval CHR_BP
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName A1 A2 EAF Beta SE Pval CHR_BP
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Column CHR_BP has been separated into the columns CHR, BP
Standardising column headers.
First line of summary statistics file:
SNP A1 A2 FRQ BETA SE P CHR BP
Checking for incorrect base-pair positions
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5864e24bf6.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.076 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c586f933665.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c587e6f5053
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c586f933665.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5865266294.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c589093b50
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName A1 A2 EAF Beta SE Pval CHR_BP CHR_BP_2
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName A1 A2 EAF Beta SE Pval CHR_BP CHR_BP_2
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Warning: Multiple columns in the sumstats file seem to relate to Chromosome:Base Pair position.
The column CHR_BP_2 will be kept whereas the column(s) CHR_BP will be removed.
If this is not the correct column to keep, please remove all incorrect columns from those listed here before
running `format_sumstats()`.
Column CHR_BP_2 has been separated into the columns CHR, BP
Standardising column headers.
First line of summary statistics file:
SNP A1 A2 FRQ BETA SE P CHR BP
Checking for incorrect base-pair positions
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5865266294.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.076 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5841985ff3.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c589093b50
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5841985ff3.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5857c418a.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58edb7feb
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5857c418a.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58a3871ac.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c587d33ad3
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58a3871ac.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Setting sorted=FALSE (required when formatted=FALSE).
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c584e2c3b11.tsv.gz
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Assigning N=1000 for all SNPs.
N already exists within sumstats_dt.
[1] "Testing: compute_n='ldsc'"
Computing effective sample size using the LDSC method:
Neff = (N_CAS+N_CON) * (N_CAS/(N_CAS+N_CON)) / mean((N_CAS/(N_CAS+N_CON))[(N_CAS+N_CON)==max(N_CAS+N_CON)]))
[1] "Testing: compute_n='giant'"
Computing effective sample size using the GIANT method:
Neff = 2 / (1/N_CAS + 1/N_CON)
[1] "Testing: compute_n='metal'"
Computing effective sample size using the METAL method:
Neff = 4 / (1/N_CAS + 1/N_CON)
[1] "Testing: compute_n='sum'"
Computing sample size using the sum method:
N = N_CAS + N_CON
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c585c231dab.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c586801160c
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c585c231dab.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5872d73180.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z
Saving output messages to:
F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z/file5c5872d73180_log_msg.txt
Any runtime errors will be saved to:
F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z/file5c5872d73180_log_output.txt
Messages will not be printed to terminal.
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c587a6759e6.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c582b3f7ea7
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c587a6759e6.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c583975571a.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58430560e8
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 186 rows
- 93 unique variants
- 140 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
93 sumstat rows are duplicated. These duplicates will be removed.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c583975571a.tsv.gz
Summary statistics report:
- 93 rows (50% of original 186 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58739130e2.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58430560e8
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58739130e2.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58f9a7aa2.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58430560e8
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 94 rows
- 94 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
1 base-pair positions are duplicated in the sumstats file. These duplicates will be removed.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Checking for bi-allelic SNPs.
Loading SNPlocs data.
Loading reference genome data.
Preprocessing RSIDs.
Validating RSIDs of 93 SNPs using BSgenome::snpsById...
BSgenome::snpsById done in 60 seconds.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58f9a7aa2.tsv.gz
Summary statistics report:
- 93 rows (98.9% of original 94 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 1.058 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58114b5608.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58ae5b58
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Filtering effect columns, ensuring none equal 0.
5 SNPs have effect values = 0 and will be removed
Ensuring all SNPs have N<5 std dev above mean.
44 SNPs (50%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58114b5608.tsv.gz
Summary statistics report:
- 88 rows (94.6% of original 93 rows)
- 88 unique variants
- 65 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.043 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58515a1221.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5871793b45
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval FRQ
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval FRQ
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs based on FRQ.
38 SNPs are below the FRQ threshold of 0.9 and will be removed.
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z/frq_filter.tsv.gz
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
55 SNPs (100%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58515a1221.tsv.gz
Summary statistics report:
- 55 rows (59.1% of original 93 rows)
- 55 unique variants
- 41 genome-wide significant variants (P<5e-8)
- 16 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 EAF BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
2: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
3: rs1008078 1 91189731 T C 0.37310 -0.016 0.003 6.005e-10
4: rs61787263 1 98618714 T C 0.76120 0.016 0.003 5.391e-08
FRQ
<num>
1: 1.863269
2: 1.169733
3: 1.401423
4: 1.873332
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5843681284.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5871793b45
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval FRQ
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval FRQ
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs based on FRQ.
38 SNPs are below the FRQ threshold of 0.9 and will be removed.
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z/frq_filter.tsv.gz
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
55 SNPs (100%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=FALSE, the FRQ column will be renamed MAJOR_ALLELE_FRQ to differentiate the values from
minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5843681284.tsv.gz
Summary statistics report:
- 55 rows (59.1% of original 93 rows)
- 55 unique variants
- 41 genome-wide significant variants (P<5e-8)
- 16 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 EAF BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
2: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
3: rs1008078 1 91189731 T C 0.37310 -0.016 0.003 6.005e-10
4: rs61787263 1 98618714 T C 0.76120 0.016 0.003 5.391e-08
MAJOR_ALLELE_FRQ
<num>
1: 1.863269
2: 1.169733
3: 1.401423
4: 1.873332
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5813932dc5.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c581bbd2950
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
SNP CHR BP A1 A2 FRQ BETA SE P
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
SNP CHR BP A1 A2 FRQ BETA SE P
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5813932dc5.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.04 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Sorting coordinates with "data.table".
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c586d5f29a6.tsv.gz
Infer Effect Column
First line of summary statistics file:
SNP CHR BP non_effect_allele effect_allele FRQ BETA1 SE P
Standardising column headers.
First line of summary statistics file:
SNP CHR BP non_effect_allele effect_allele FRQ BETA1 SE P
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c586d5f29a6.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.038 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning data directly.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5855ea7029.tsv.gz
Infer Effect Column
First line of summary statistics file:
SNP CHR BP A2 A1 FRQ BETA1 SE P
Allele columns are ambiguous, attempting to infer direction
Found direction from effect/frq column naming
Standardising column headers.
First line of summary statistics file:
SNP CHR BP A2 A1 FRQ BETA1 SE P
Effect/frq column(s) relate to A1 in the sumstat
Standardising column headers.
First line of summary statistics file:
SNP CHR BP A1 A2 FRQ BETA1 SE P
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5855ea7029.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.075 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning data directly.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c587e5c3b00.tsv.gz
Infer Effect Column
First line of summary statistics file:
SNP CHR BP A2 A1 A1FRQ BETA SE P
Allele columns are ambiguous, attempting to infer direction
Found direction from effect/frq column naming
Standardising column headers.
First line of summary statistics file:
SNP CHR BP A2 A1 A1FRQ BETA SE P
Effect/frq column(s) relate to A1 in the sumstat
Standardising column headers.
First line of summary statistics file:
SNP CHR BP A1 A2 A1FRQ BETA SE P
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c587e5c3b00.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.093 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning data directly.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58410848d6.tsv.gz
Infer Effect Column
First line of summary statistics file:
SNP CHR BP A2 A1 FRQ BETA SE P
Allele columns are ambiguous, attempting to infer direction
Standardising column headers.
First line of summary statistics file:
SNP CHR BP A2 A1 FRQ BETA SE P
Loading SNPlocs data.
Loading reference genome data.
Preprocessing RSIDs.
Validating RSIDs of 76 SNPs using BSgenome::snpsById...
BSgenome::snpsById done in 30 seconds.
Effect/frq column(s) relate to A1 in the inputted sumstats
Found direction from matching reference genome - NOTE this assumes non-effect allele will match the reference genome
Standardising column headers.
First line of summary statistics file:
SNP CHR BP A1 A2 FRQ BETA SE P
Summary statistics report:
- 76 rows
- 76 unique variants
- 55 genome-wide significant variants (P<5e-8)
- 19 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Ensuring all SNPs are on the reference genome.
Loading SNPlocs data.
Loading reference genome data.
Preprocessing RSIDs.
Validating RSIDs of 76 SNPs using BSgenome::snpsById...
BSgenome::snpsById done in 30 seconds.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
41 SNPs (53.9%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58410848d6.tsv.gz
Summary statistics report:
- 76 rows (100% of original 76 rows)
- 76 unique variants
- 55 genome-wide significant variants (P<5e-8)
- 19 chromosomes
Done munging in 1.11 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs114598875 2 60976384 A G 0.8246 -0.020 0.004 2.405e-08
2: rs13402908 2 100333377 T C 0.5056 -0.018 0.003 1.695e-11
3: rs34106693 2 101151830 C G 0.8190 0.020 0.004 7.527e-08
4: rs17824247 2 144152539 T C 0.5802 -0.016 0.003 2.766e-09
Returning data directly.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c584fb672ac.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5860aa6a3b
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval INFO
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval INFO
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
Filtering SNPs based on INFO score.
38 SNPs are below the INFO threshold of 0.9 and will be removed.
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z/info_filter.tsv.gz
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
28 SNPs (50.9%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c584fb672ac.tsv.gz
Summary statistics report:
- 55 rows (59.1% of original 93 rows)
- 55 unique variants
- 41 genome-wide significant variants (P<5e-8)
- 16 chromosomes
Done munging in 0.043 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
2: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
3: rs1008078 1 91189731 T C 0.37310 -0.016 0.003 6.005e-10
4: rs61787263 1 98618714 T C 0.76120 0.016 0.003 5.391e-08
INFO
<num>
1: 1.863269
2: 1.169733
3: 1.401423
4: 1.873332
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c583dff25ce.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58299d208e
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c583dff25ce.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5863f553d7.tsv.gz
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5863f553d7.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.038 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
[1] "F:\\biocbuild\\bbs-3.20-bioc-longtests\\tmpdir\\RtmpgPbe2Z/data/file1\\file5c5837f45118.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.20-bioc-longtests\\tmpdir\\RtmpgPbe2Z/data/file2\\file5c585f97c5f.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.20-bioc-longtests\\tmpdir\\RtmpgPbe2Z/data/file3\\file5c58583f4cd6.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.20-bioc-longtests\\tmpdir\\RtmpgPbe2Z/data/file4\\file5c5846194629.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.20-bioc-longtests\\tmpdir\\RtmpgPbe2Z/data/file5\\file5c586f9d6ec8.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.20-bioc-longtests\\tmpdir\\RtmpgPbe2Z/data/file6\\file5c5855643127.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.20-bioc-longtests\\tmpdir\\RtmpgPbe2Z/data/file7\\file5c587b4e1ff8.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.20-bioc-longtests\\tmpdir\\RtmpgPbe2Z/data/file8\\file5c58164a7d53.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.20-bioc-longtests\\tmpdir\\RtmpgPbe2Z/data/file9\\file5c58457123dc.tsv.gz"
[1] "F:\\biocbuild\\bbs-3.20-bioc-longtests\\tmpdir\\RtmpgPbe2Z/data/file10\\file5c5818fb2a6d.tsv.gz"
10 file(s) found.
Parsing info from 10 log file(s).
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c582a0430eb.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58c7f5224
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 92 unique variants
- 69 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
WARNING: 1 rows in sumstats file are missing data and will be removed.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
46 SNPs (50%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c582a0430eb.tsv.gz
Summary statistics report:
- 92 rows (98.9% of original 93 rows)
- 92 unique variants
- 69 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs10061788 5 87934707 A G 0.2164 0.021 0.004 2.464e-09
2: rs1007883 16 51163406 T C 0.3713 -0.015 0.003 5.326e-08
3: rs1008078 1 91189731 T C 0.3731 -0.016 0.003 6.005e-10
4: rs1043209 14 23373986 A G 0.6026 0.018 0.003 1.816e-11
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58258a6e3.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58c7f5224
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58258a6e3.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs10061788 5 87934707 A G 0.2164 0.021 0.004 2.464e-09
2: rs1007883 16 51163406 T C 0.3713 -0.015 0.003 5.326e-08
3: rs1008078 1 91189731 T C 0.3731 -0.016 0.003 6.005e-10
4: rs1043209 14 23373986 A G 0.6026 0.018 0.003 1.816e-11
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5870d53853.tsv.gz
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 21 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Loading SNPlocs data.
There is no Chromosome or Base Pair Position column found within the data. It must be inferred from other column information.
Loading reference genome data.
Preprocessing RSIDs.
Validating RSIDs of 1 SNPs using BSgenome::snpsById...
BSgenome::snpsById done in 2 seconds.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5870d53853.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.083 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs10061788 5 87934707 A G 0.2164 0.021 0.004 2.464e-09
2: rs1007883 16 51163406 T C 0.3713 -0.015 0.003 5.326e-08
3: rs1008078 1 91189731 T C 0.3731 -0.016 0.003 6.005e-10
4: rs1043209 14 23373986 A G 0.6026 0.018 0.003 1.816e-11
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c581fc53348.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5819502c36
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
chromosome rs_id markername position_hg18 Effect_allele Other_allele EAF_HapMapCEU N_SMK Effect_SMK StdErr_SMK P_value_SMK N_NONSMK Effect_NonSMK StdErr_NonSMK P_value_NonSMK
Standardising column headers.
First line of summary statistics file:
chromosome rs_id markername position_hg18 Effect_allele Other_allele EAF_HapMapCEU N_SMK Effect_SMK StdErr_SMK P_value_SMK N_NONSMK Effect_NonSMK StdErr_NonSMK P_value_NonSMK
Summary statistics report:
- 5 rows
- 5 unique variants
- 1 chromosomes
Checking for multi-GWAS.
WARNING: Multiple traits found in sumstats file only one of which can be analysed:
SMK, NONSMK
Standardising column headers.
First line of summary statistics file:
CHR SNP MARKERNAME POSITION_HG18 A2 A1 EAF_HAPMAPCEU N EFFECT STDERR P_VALUE N_NONSMK EFFECT_NONSMK STDERR_NONSMK P_VALUE_NONSMK
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
1 SNP IDs are not correctly formatted and will be removed.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column.
Column MARKERNAME has been separated into the columns CHR, BP
Standardising column headers.
First line of summary statistics file:
CHR SNP POSITION_HG18 A2 A1 EAF_HAPMAPCEU N BETA SE P N_NONSMK EFFECT_NONSMK STDERR_NONSMK P_VALUE_NONSMK BP
Checking for incorrect base-pair positions
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Ensuring that the N column is all integers.
The sumstats N column is not all integers, this could effect downstream analysis. These will be converted to integers.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c581fc53348.tsv.gz
Summary statistics report:
- 4 rows (80% of original 5 rows)
- 4 unique variants
- 0 genome-wide significant variants (P<5e-8)
- 1 chromosomes
Done munging in 0.114 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 POSITION_HG18 EAF_HAPMAPCEU N
<char> <char> <int> <char> <char> <int> <num> <int>
1: rs1000050 chr1 161003087 C T 161003087 0.9000 36257
2: rs1000073 chr1 155522020 G A 155522020 0.3136 36335
3: rs1000075 chr1 94939420 C T 94939420 0.3583 38959
4: rs1000085 chr1 66630503 G C 66630503 0.1667 38761
BETA SE P N_NONSMK EFFECT_NONSMK STDERR_NONSMK P_VALUE_NONSMK
<num> <num> <num> <int> <num> <num> <num>
1: 0.0001 0.0109 0.9931 127514 0.0058 0.0059 0.3307
2: 0.0046 0.0083 0.5812 126780 0.0038 0.0045 0.3979
3: -0.0013 0.0082 0.8687 147567 -0.0043 0.0044 0.3259
4: 0.0053 0.0095 0.5746 147259 -0.0034 0.0052 0.5157
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5868594a22.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c589487889
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval N N_fixed
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval N N_fixed
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Ensuring that the N column is all integers.
The sumstats N column is not all integers, this could effect downstream analysis. These will be converted to integers.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5868594a22.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P N
<char> <int> <int> <char> <char> <num> <num> <num> <num> <int>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08 5
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10 1
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14 1
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08 7
N_FIXED
<int>
1: 5
2: 1
3: 1
4: 7
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c582bb030e9.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c582daa4cdc
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval N
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval N
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
The sumstats N column is not all integers, this could effect downstream analysis.These will NOT be converted to integers.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
1 SNPs have N values 5 standard deviations above the mean and will be removed
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z/n_large.tsv.gz
47 SNPs (51.1%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c582bb030e9.tsv.gz
Summary statistics report:
- 92 rows (98.9% of original 93 rows)
- 92 unique variants
- 69 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P N
<char> <int> <int> <char> <char> <num> <num> <num> <num> <int>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08 3
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10 5
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14 3
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08 3
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5836b46b77.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c582daa4cdc
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval N
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval N
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
The sumstats N column is not all integers, this could effect downstream analysis.These will NOT be converted to integers.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
1 SNPs have N values 5 standard deviations above the mean and will be removed
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z/n_large.tsv.gz
47 SNPs (51.1%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5836b46b77.tsv.gz
Summary statistics report:
- 92 rows (98.9% of original 93 rows)
- 92 unique variants
- 69 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P N
<char> <int> <int> <char> <char> <num> <num> <num> <num> <int>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08 3
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10 5
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14 3
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08 3
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c587e5491.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c582daa4cdc
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval N
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval N
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
The sumstats N column is not all integers, this could effect downstream analysis.These will NOT be converted to integers.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
1 SNPs have N values 5 standard deviations above the mean and will be removed
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z/n_large.tsv.gz
Removing rows where is.na(N)
0 SNPs have N values that are NA and will be removed.
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z/n_null.tsv.gz
47 SNPs (51.1%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c587e5491.tsv.gz
Summary statistics report:
- 92 rows (98.9% of original 93 rows)
- 92 unique variants
- 69 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P N
<char> <int> <int> <char> <char> <num> <num> <num> <num> <int>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08 3
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10 5
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14 3
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08 3
Returning path to saved data.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c581c944b6e.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c583d686719
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 23 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
1 SNPs have been removed as their BP column is not in the range of 1 to the length of the chromosome
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z/bad_bp.tsv.gz
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
2 SNPs are on chromosomes X, Y, MT and will be removed.
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z/chr_excl.tsv.gz
45 SNPs (50%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c581c944b6e.tsv.gz
Summary statistics report:
- 90 rows (96.8% of original 93 rows)
- 90 unique variants
- 67 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.04 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58782e4bd9.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c583d686719
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58782e4bd9.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c587033df9
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
SNP CHR BP A1 A2 FRQ BETA SE P
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c581e6e77a0
Checking for empty columns.
Standardising column headers.
First line of summary statistics file:
SNP CHR BP A1 A2 FRQ BETA SE P
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5840e62990.vcf.bgz
Sorting coordinates with "data.table".
Converting summary statistics to GenomicRanges.
Converting summary statistics to VRanges.
Writing in VCF format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5840e62990.vcf.bgz
Loading required namespace: GenomicFiles
Using local VCF.
Finding empty VCF columns based on first 10,000 rows.
1 sample detected: GWAS
Constructing ScanVcfParam object.
Reading VCF file: single-threaded
Converting VCF to data.table.
Expanding VCF first, so number of rows may increase.
Checking for empty columns.
Time difference of 0.1 secs
VCF data.table contains: 93 rows x 11 columns.
Time difference of 0.4 secs
No INFO (SI) column detected.
Standardising column headers.
First line of summary statistics file:
ID chr BP end REF ALT SNP FRQ BETA SE P
Using local VCF.
bgzip-compressing VCF file.
Finding empty VCF columns based on first 10,000 rows.
Dropping 1 duplicate column(s).
1 sample detected: EBI-a-GCST005647
Constructing ScanVcfParam object.
VCF contains: 39,630,630 variant(s) x 1 sample(s)
Reading VCF file: single-threaded
Converting VCF to data.table.
Expanding VCF first, so number of rows may increase.
Dropping 1 duplicate column(s).
Checking for empty columns.
Unlisting 3 columns.
Dropped 314 duplicate rows.
Time difference of 0.1 secs
VCF data.table contains: 101 rows x 11 columns.
Time difference of 0.4 secs
Renaming ID as SNP.
sumstats has -log10 P-values; these will be converted to unadjusted p-values in the 'P' column.
No INFO (SI) column detected.
Standardising column headers.
First line of summary statistics file:
SNP chr BP end REF ALT FILTER AF ES LP SE P
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c583f4a3b4e.vcf.bgz
Sorting coordinates with "data.table".
Converting summary statistics to GenomicRanges.
Converting summary statistics to VRanges.
Writing in VCF format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c583f4a3b4e.vcf.bgz
Using local VCF.
Finding empty VCF columns based on first 10,000 rows.
1 sample detected: GWAS
Constructing ScanVcfParam object.
Reading VCF file: single-threaded
Converting VCF to data.table.
Expanding VCF first, so number of rows may increase.
Checking for empty columns.
Time difference of 0.1 secs
VCF data.table contains: 101 rows x 13 columns.
Time difference of 0.3 secs
sumstats has -log10 P-values; these will be converted to unadjusted p-values in the 'P' column.
No INFO (SI) column detected.
Standardising column headers.
First line of summary statistics file:
ID chr BP end REF SNP END FILTER FRQ BETA LP SE P
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c582a46845.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z
Infer Effect Column
First line of summary statistics file:
SNP P FRQ BETA CHR BP
Standardising column headers.
First line of summary statistics file:
SNP P FRQ BETA CHR BP
Summary statistics report:
- 5 rows
- 5 unique variants
- 0 genome-wide significant variants (P<5e-8)
- 1 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
5 SNP IDs contain other information in the same column. These will be separated.
Checking for merged allele column.
Column SNP_INFO has been separated into the columns A1, A2
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Coercing BP column to numeric.
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
SE is not present but can be imputed with BETA & P. Set impute_se=TRUE and rerun to do this.
Ensuring all SNPs have N<5 std dev above mean.
3 SNPs (60%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c582a46845.tsv.gz
Summary statistics report:
- 5 rows (100% of original 5 rows)
- 5 unique variants
- 0 genome-wide significant variants (P<5e-8)
- 1 chromosomes
Done munging in 0.038 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 P FRQ BETA
<char> <int> <int> <char> <char> <num> <num> <num>
1: rs140052487 1 54353 C A 0.037219838 0.3000548 0.8797957
2: rs558796213 1 54564 G T 0.004382482 0.5848666 0.7068747
3: rs561234294 1 54591 A G 0.070968402 0.3334671 0.7319726
4: rs2462492 1 54676 C T 0.065769040 0.6220120 0.9316344
Returning data directly.
******::NOTE::******
- Log results will be saved to `tempdir()` by default.
- This means all log data from the run will be deleted upon ending the R session.
- To keep it, change `log_folder` to an actual directory (e.g. log_folder='./').
********************
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58193a6a2a.tsv.gz
Log data to be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z
Infer Effect Column
First line of summary statistics file:
SNP P FRQ BETA CHR BP A1 A2
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
SNP P FRQ BETA CHR BP A1 A2
Summary statistics report:
- 5 rows
- 5 unique variants
- 0 genome-wide significant variants (P<5e-8)
- 1 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Coercing BP column to numeric.
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
SE is not present but can be imputed with BETA & P. Set impute_se=TRUE and rerun to do this.
Ensuring all SNPs have N<5 std dev above mean.
3 SNPs (60%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58193a6a2a.tsv.gz
Summary statistics report:
- 5 rows (100% of original 5 rows)
- 5 unique variants
- 0 genome-wide significant variants (P<5e-8)
- 1 chromosomes
Done munging in 0.039 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 P FRQ BETA
<char> <int> <int> <char> <char> <num> <num> <num>
1: rs140052487 1 54353 C A 0.037219838 0.3000548 0.8797957
2: rs558796213 1 54564 G T 0.004382482 0.5848666 0.7068747
3: rs561234294 1 54591 A G 0.070968402 0.3334671 0.7319726
4: rs2462492 1 54676 C T 0.065769040 0.6220120 0.9316344
Returning data directly.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c587f6452f4.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c585c75350e
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c588f1573a.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c584ec7312b
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c588f1573a.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.04 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58535d5e.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c584ec7312b
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58535d5e.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.04 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58414d539b.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5816c44392
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58414d539b.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.04 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c581826607d.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c583137776
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
47 SNPs (50.5%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c581826607d.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.04 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58567d3b27.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c584b1e6322
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
5 SNPs have SE values <= 0 and will be removed
Ensuring all SNPs have N<5 std dev above mean.
44 SNPs (50%) have FRQ values > 0.5. Conventionally the FRQ column is intended to show the minor/effect allele frequency.
The FRQ column was mapped from one of the following from the inputted summary statistics file:
FRQ, EAF, FREQUENCY, FRQ_U, F_U, MAF, FREQ, FREQ_TESTED_ALLELE, FRQ_TESTED_ALLELE, FREQ_EFFECT_ALLELE, FRQ_EFFECT_ALLELE, EFFECT_ALLELE_FREQUENCY, EFFECT_ALLELE_FREQ, EFFECT_ALLELE_FRQ, A2FREQ, A2FRQ, ALLELE_FREQUENCY, ALLELE_FREQ, ALLELE_FRQ, AF, MINOR_AF, EFFECT_AF, A2_AF, EFF_AF, ALT_AF, ALTERNATIVE_AF, INC_AF, A_2_AF, TESTED_AF, ALLELEFREQ, ALT_FREQ, EAF_HRC, EFFECTALLELEFREQ, FREQ.B, FREQ_EUROPEAN_1000GENOMES, FREQ_HAPMAP, FREQ_TESTED_ALLELE_IN_HRS, FRQ_U_113154, FRQ_U_31358, FRQ_U_344901, FRQ_U_43456, POOLED_ALT_AF, AF_ALT, AF.ALT, AF-ALT, ALT.AF, ALT-AF, A2.AF, A2-AF, AF.EFF, AF_EFF, ALL_AF
As frq_is_maf=TRUE, the FRQ column will not be renamed. If the FRQ values were intended to represent major allele frequency,
set frq_is_maf=FALSE to rename the column as MAJOR_ALLELE_FRQ and differentiate it from minor/effect allele frequency.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58567d3b27.tsv.gz
Summary statistics report:
- 88 rows (94.6% of original 93 rows)
- 88 unique variants
- 65 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.055 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 FRQ BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning path to saved data.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval Support
Returning unmapped column names without making them uppercase.
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval Support
Returning unmapped column names without making them uppercase.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c581b236671.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5827d7288.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c586ca71ae4
Checking for empty columns.
Non-standard mapping file detected.Making sure all entries in `Uncorrected` are in upper case.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Summary statistics report:
- 93 rows
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Checking for missing data.
Checking for duplicate columns.
Checking for duplicated rows.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Sorting coordinates with "data.table".
Writing in tabular format ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5827d7288.tsv.gz
Summary statistics report:
- 93 rows (100% of original 93 rows)
- 93 unique variants
- 70 genome-wide significant variants (P<5e-8)
- 20 chromosomes
Done munging in 0.04 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
SNP CHR BP A1 A2 EAF BETA SE P
<char> <int> <int> <char> <char> <num> <num> <num> <num>
1: rs301800 1 8490603 T C 0.17910 0.019 0.003 1.794e-08
2: rs11210860 1 43982527 A G 0.36940 0.017 0.003 2.359e-10
3: rs34305371 1 72733610 A G 0.08769 0.035 0.005 3.762e-14
4: rs2568955 1 72762169 T C 0.23690 -0.017 0.003 1.797e-08
Returning data directly.
Converting summary statistics to GenomicRanges.
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5867f17b03.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5811ad1780.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c583c433034.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c585ee35fc5.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5871001196.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5843323b6.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5853d0397f.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5825a96bfa.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58114b2e7b.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58db4711a.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c58136817ef.tsv.gz
Formatted summary statistics will be saved to ==> F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5826e1abf.tsv.gz
Reading header.
Tabular format detected.
Importing tabular file: F:\biocbuild\bbs-3.20-bioc-longtests\tmpdir\RtmpgPbe2Z\file5c5844886f1
Checking for empty columns.
Infer Effect Column
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE
Allele columns are ambiguous, attempting to infer direction
Can't infer allele columns from sumstats
Standardising column headers.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE
Summary statistics report:
- 93 rows
- 93 unique variants
- 20 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
[ FAIL 0 | WARN 2 | SKIP 1 | PASS 146 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-write_sumstats.R:1:1'
[ FAIL 0 | WARN 2 | SKIP 1 | PASS 146 ]
>
> proc.time()
user system elapsed
302.87 10.40 327.29
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no MungeSumstats_1.14.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.20-bioc-longtests/meat/MungeSumstats.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using options '--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error'
* checking for file 'MungeSumstats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MungeSumstats' version '1.14.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'MungeSumstats' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) check_no_chr_bp.Rd:56-57: Lost braces
56 | \item \code{sumstats_dt}{
| ^
checkRd: (-1) check_no_chr_bp.Rd:58-59: Lost braces
58 | \item \code{rsids}{
| ^
checkRd: (-1) check_no_chr_bp.Rd:60-61: Lost braces
60 | \item \code{log_files}{
| ^
checkRd: (-1) check_on_ref_genome.Rd:65-66: Lost braces
65 | \item \code{sumstats_dt}{
| ^
checkRd: (-1) check_on_ref_genome.Rd:67-68: Lost braces
67 | \item \code{rsids}{
| ^
checkRd: (-1) check_on_ref_genome.Rd:69-70: Lost braces
69 | \item \code{log_files}{
| ^
checkRd: (-1) compute_nsize.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_nsize.Rd:33-36: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_nsize.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_nsize.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_nsize.Rd:41-42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_nsize.Rd:43-44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size.Rd:21-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size.Rd:30-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size.Rd:36-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size.Rd:42-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size.Rd:48-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_n.Rd:16-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_n.Rd:25-29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_n.Rd:31-35: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_n.Rd:37-41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_n.Rd:43-47: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_neff.Rd:21-28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_neff.Rd:30-34: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_neff.Rd:36-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_neff.Rd:42-46: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_sample_size_neff.Rd:48-52: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_sumstats.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_sumstats.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_sumstats.Rd:31-32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_vcf.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_vcf.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_vcf.Rd:66-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_vcf_parallel.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_vcf_parallel.Rd:41: Lost braces in \itemize; meant \describe ?
checkRd: (-1) read_vcf_parallel.Rd:42-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) select_vcf_fields.Rd:27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) select_vcf_fields.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) select_vcf_fields.Rd:29-30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_coords.Rd:19-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) sort_coords.Rd:22-24: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... SKIPPED
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... SKIPPED
* checking examples ... SKIPPED
* checking for unstated dependencies in 'longtests' ... OK
* checking tests in 'longtests' ...
Running 'testthat.R'
OK
* DONE
Status: 2 NOTEs
See
'F:/biocbuild/bbs-3.20-bioc-longtests/meat/MungeSumstats.Rcheck/00check.log'
for details.
MungeSumstats.Rcheck/00install.out
* installing *source* package 'MungeSumstats' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MungeSumstats)