Alan Murphy
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/MungeSumstats |
| git_branch: RELEASE_3_13 |
| git_last_commit: c1fe775 |
| git_last_commit_date: 2021-06-22 14:02:24 -0400 (Tue, 22 Jun 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:13 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the MungeSumstats package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MungeSumstats.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1232/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MungeSumstats 1.0.1 (landing page) Alan Murphy
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: MungeSumstats |
| Version: 1.0.1 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MungeSumstats.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MungeSumstats_1.0.1.tar.gz |
| StartedAt: 2021-10-15 02:30:13 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 02:39:29 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 555.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MungeSumstats.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MungeSumstats.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MungeSumstats_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MungeSumstats.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MungeSumstats/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MungeSumstats' version '1.0.1'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'MungeSumstats' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* 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' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
format_sumstats 24.91 3.34 72.21
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
MungeSumstats.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MungeSumstats_1.0.1.tar.gz && rm -rf MungeSumstats.buildbin-libdir && mkdir MungeSumstats.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MungeSumstats.buildbin-libdir MungeSumstats_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MungeSumstats_1.0.1.zip && rm MungeSumstats_1.0.1.tar.gz MungeSumstats_1.0.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 89684 100 89684 0 0 560k 0 --:--:-- --:--:-- --:--:-- 565k
install for i386
* installing *source* package 'MungeSumstats' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'MungeSumstats'
finding HTML links ... done
check_allele_flip html
check_allele_merge html
check_bi_allelic html
check_chr html
check_col_order html
check_dup_bp html
check_dup_col html
check_dup_snp html
check_four_step_col html
check_info_score html
check_miss_data html
check_multi_gwas html
check_n_int html
check_n_num html
check_no_allele html
check_no_chr_bp html
check_no_rs_snp html
check_no_snp html
check_on_ref_genome html
check_row_snp html
check_signed_col html
check_small_p_val html
check_strand_ambiguous html
check_tab_delimited html
check_two_step_col html
check_vcf html
check_vital_col html
format_sumstats html
load_ref_genome_data html
load_snp_loc_data html
raw_ALSvcf html
raw_eduAttainOkbay html
standardise_sumstats_column_headers_crossplatform
html
sumstatsColHeaders html
validate_parameters html
** 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
install for x64
* installing *source* package 'MungeSumstats' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MungeSumstats' as MungeSumstats_1.0.1.zip
* DONE (MungeSumstats)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MungeSumstats' successfully unpacked and MD5 sums checked
|
MungeSumstats.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
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")
First line of summary statistics file:
MarkerName EAF Beta SE Pval CHR_BP_A2_A1
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
First line of summary statistics file:
SNP FRQ BETA SE P CHR BP A2 A1
Reordering so first three column headers are SNP, CHR and BP in this order.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP FRQ BETA SE P A2 A1
rs13402908 2 100333377 0.5056 -0.018 0.003 1.695e-11 C T
rs113081851 13 100664477 0.3265 -0.015 0.003 9.829e-08 C T
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName EAF Beta SE Pval CHR_BP_A2_A1 CHR_BP_A2_A1_2
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:A2:A1.
The column CHR_BP_A2_A1_2 will be kept whereas the column(s) CHR_BP_A2_A1 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_A2_A1_2 has been separated into the columns CHR, BP, A2, A1
First line of summary statistics file:
SNP FRQ BETA SE P CHR BP A2 A1
Reordering so first three column headers are SNP, CHR and BP in this order.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP FRQ BETA SE P A2 A1
rs13402908 2 100333377 0.5056 -0.018 0.003 1.695e-11 C T
rs113081851 13 100664477 0.3265 -0.015 0.003 9.829e-08 C T
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS EAF Beta SE Pval alleles allele
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
Succesfully finished preparing sumstats file, preview:
SNP CHR BP FRQ BETA SE P A1 A2
rs12646808 4 3249828 0.6418 0.016 0.003 4.002e-08 T C
rs301800 1 8490603 0.1791 0.019 0.003 1.794e-08 T C
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName A1 A2 EAF Beta SE Pval CHR_BP
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
First line of summary statistics file:
SNP A1 A2 FRQ BETA SE P CHR BP
Reordering so first three column headers are SNP, CHR and BP in this order.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs13402908 2 100333377 T C 0.5056 -0.018 0.003 1.695e-11
rs113081851 13 100664477 T C 0.3265 -0.015 0.003 9.829e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName A1 A2 EAF Beta SE Pval CHR_BP CHR_BP_2
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
First line of summary statistics file:
SNP A1 A2 FRQ BETA SE P CHR BP
Reordering so first three column headers are SNP, CHR and BP in this order.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs13402908 2 100333377 T C 0.5056 -0.018 0.003 1.695e-11
rs113081851 13 100664477 T C 0.3265 -0.015 0.003 9.829e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
WARNING: GWAS sumstat file has comma field separators instead of tabs (unusual, not proper input for MAGMA).
Temp file with corrected FS created and used instead.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
93 RS IDs are duplicated in the sumstats file. These duplicates will be removed
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
1 base-pair Positions are duplicated in the sumstats file. These duplicates will be removed
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
SNP CHR BP A1 A2 FRQ BETA SE P
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval INFO
38 SNPs are below the INFO threshold of 0.9 and will be removed
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P INFO
rs76076331 2 10977585 T C 0.09328 0.02 0.004 3.632e-08 1.21987180458382
rs7945718 11 12748819 A G 0.5951 0.015 0.003 1.54e-08 1.52137891063467
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
WARNING: 1 rows in sumstats file are missing data and will be removed.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
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
WARNING: Multiple traits found in sumstats file only one of which can be analysed:
SMK, NONSMK
First line of summary statistics file:
CHR SNP MARKERNAME POSITION_HG18 A1 A2 EAF_HAPMAPCEU N EFFECT STDERR P_VALUE N_NONSMK EFFECT_NONSMK STDERR_NONSMK P_VALUE_NONSMK
1 SNP IDs are not correctly formatted and will be removed
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
First line of summary statistics file:
CHR SNP POSITION_HG18 A1 A2 EAF_HAPMAPCEU N BETA STDERR P N_NONSMK EFFECT_NONSMK STDERR_NONSMK P_VALUE_NONSMK BP
Reordering so first three column headers are SNP, CHR and BP in this order.
The sumstats N column is not all integers, this could effect downstream analysis.These will be converted to integers.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP POSITION_HG18 A1 A2 EAF_HAPMAPCEU N BETA STDERR P N_NONSMK EFFECT_NONSMK STDERR_NONSMK P_VALUE_NONSMK
rs1000073 chr1 155522020 155522020 A G 0.3136 36335 0.0046 0.0083 0.5812 126780 0.0038 0.0045 0.3979
rs1000050 chr1 161003087 161003087 T C 0.9 36257 1e-04 0.0109 0.9931 127514 0.0058 0.0059 0.3307
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval N N_fixed
The sumstats N column is not all integers, this could effect downstream analysis.These will be converted to integers.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P N N_FIXED
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08 9 9
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08 5 5
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval N
The sumstats N column is not all integers, this could effect downstream analysis.These will NOT be converted to integers.
1 SNPs have N values 5 standard deviations above the mean and will be removed
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P N
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08 2
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08 3
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
3 SNPs are on chromosomes X, Y, MT and will be removed
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF SE Pval
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
There are existing p-values as low as 5e-324 which LDSC/MAGMA may not be able to handle. These will be converted to 0.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
WARNING: GWAS sumstat file has space field separators instead of tabs (unusual, not proper input for MAGMA).
Temp file with corrected FS created and used instead.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
VCF format detected, this will be converted to a standard summary statistics file format.
Inputted VCF format has -log10 P-values, these will be converted to unadjusted p-values in the 'P' column.
First line of summary statistics file:
CHROM POS REF ALT INFO ES SE LP AF ID P
Reordering so first three column headers are SNP, CHR and BP in this order.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 INFO BETA SE LP AF P
rs58108140 1 10583 G A 0.1589 0.0312 0.0393 0.369267 0.1589 0.427300105456596
rs806731 1 30923 G T 0.7843 -0.0114 0.0353 0.126854 0.7843 0.746699739815279
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 48 ]
>
> proc.time()
user system elapsed
10.39 1.37 17.15
|
MungeSumstats.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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")
First line of summary statistics file:
MarkerName CHR POS A2 A1 EAF Beta SE Pval
There are more matches to the reference genome found when the alleles are flipped.
These will be flipped along with the effect column.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
1 SNPs are non-biallelic. These will be removed
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs10061788 5 87934707 A G 0.2164 0.021 0.004 2.464e-09
rs1007883 16 51163406 T C 0.3713 -0.015 0.003 5.326e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName EAF Beta SE Pval CHR_BP_A2_A1
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
First line of summary statistics file:
SNP FRQ BETA SE P CHR BP A2 A1
Reordering so first three column headers are SNP, CHR and BP in this order.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP FRQ BETA SE P A2 A1
rs13402908 2 100333377 0.5056 -0.018 0.003 1.695e-11 C T
rs113081851 13 100664477 0.3265 -0.015 0.003 9.829e-08 C T
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName EAF Beta SE Pval CHR_BP_A2_A1 CHR_BP_A2_A1_2
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:A2:A1.
The column CHR_BP_A2_A1_2 will be kept whereas the column(s) CHR_BP_A2_A1 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_A2_A1_2 has been separated into the columns CHR, BP, A2, A1
First line of summary statistics file:
SNP FRQ BETA SE P CHR BP A2 A1
Reordering so first three column headers are SNP, CHR and BP in this order.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP FRQ BETA SE P A2 A1
rs13402908 2 100333377 0.5056 -0.018 0.003 1.695e-11 C T
rs113081851 13 100664477 0.3265 -0.015 0.003 9.829e-08 C T
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS EAF Beta SE Pval alleles allele
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
Succesfully finished preparing sumstats file, preview:
SNP CHR BP FRQ BETA SE P A1 A2
rs12646808 4 3249828 0.6418 0.016 0.003 4.002e-08 T C
rs301800 1 8490603 0.1791 0.019 0.003 1.794e-08 T C
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName A1 A2 EAF Beta SE Pval CHR_BP
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
First line of summary statistics file:
SNP A1 A2 FRQ BETA SE P CHR BP
Reordering so first three column headers are SNP, CHR and BP in this order.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs13402908 2 100333377 T C 0.5056 -0.018 0.003 1.695e-11
rs113081851 13 100664477 T C 0.3265 -0.015 0.003 9.829e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName A1 A2 EAF Beta SE Pval CHR_BP CHR_BP_2
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
First line of summary statistics file:
SNP A1 A2 FRQ BETA SE P CHR BP
Reordering so first three column headers are SNP, CHR and BP in this order.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs13402908 2 100333377 T C 0.5056 -0.018 0.003 1.695e-11
rs113081851 13 100664477 T C 0.3265 -0.015 0.003 9.829e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
WARNING: GWAS sumstat file has comma field separators instead of tabs (unusual, not proper input for MAGMA).
Temp file with corrected FS created and used instead.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
93 RS IDs are duplicated in the sumstats file. These duplicates will be removed
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
1 base-pair Positions are duplicated in the sumstats file. These duplicates will be removed
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
SNP CHR BP A1 A2 FRQ BETA SE P
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval INFO
38 SNPs are below the INFO threshold of 0.9 and will be removed
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P INFO
rs76076331 2 10977585 T C 0.09328 0.02 0.004 3.632e-08 1.21987180458382
rs7945718 11 12748819 A G 0.5951 0.015 0.003 1.54e-08 1.52137891063467
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
WARNING: 1 rows in sumstats file are missing data and will be removed.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
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
WARNING: Multiple traits found in sumstats file only one of which can be analysed:
SMK, NONSMK
First line of summary statistics file:
CHR SNP MARKERNAME POSITION_HG18 A1 A2 EAF_HAPMAPCEU N EFFECT STDERR P_VALUE N_NONSMK EFFECT_NONSMK STDERR_NONSMK P_VALUE_NONSMK
1 SNP IDs are not correctly formatted and will be removed
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
First line of summary statistics file:
CHR SNP POSITION_HG18 A1 A2 EAF_HAPMAPCEU N BETA STDERR P N_NONSMK EFFECT_NONSMK STDERR_NONSMK P_VALUE_NONSMK BP
Reordering so first three column headers are SNP, CHR and BP in this order.
The sumstats N column is not all integers, this could effect downstream analysis.These will be converted to integers.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP POSITION_HG18 A1 A2 EAF_HAPMAPCEU N BETA STDERR P N_NONSMK EFFECT_NONSMK STDERR_NONSMK P_VALUE_NONSMK
rs1000073 chr1 155522020 155522020 A G 0.3136 36335 0.0046 0.0083 0.5812 126780 0.0038 0.0045 0.3979
rs1000050 chr1 161003087 161003087 T C 0.9 36257 1e-04 0.0109 0.9931 127514 0.0058 0.0059 0.3307
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval N N_fixed
The sumstats N column is not all integers, this could effect downstream analysis.These will be converted to integers.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P N N_FIXED
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08 9 9
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08 5 5
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval N
The sumstats N column is not all integers, this could effect downstream analysis.These will NOT be converted to integers.
1 SNPs have N values 5 standard deviations above the mean and will be removed
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P N
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08 2
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08 3
First line of summary statistics file:
MarkerName CHR POS EAF Beta SE Pval
There is no A1 or A2 allele information column found within the data. It must be inferred from other column information.
Deriving both A1 and A2 from reference genome
WARNING: Inferring the alternative allele (A2) from the reference genome. In some instances, there are more than one
alternative allele. Arbitrarily, only the first will be kept. See column `alt_alleles` in your returned sumstats file
for all alternative alleles.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P alt_alleles
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08 C
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08 C
First line of summary statistics file:
MarkerName CHR POS A2 EAF Beta SE Pval
There is no A1 or A2 allele information column found within the data. It must be inferred from other column information.
Deriving A1 from reference genome
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 EAF Beta SE Pval
There is no A1 or A2 allele information column found within the data. It must be inferred from other column information.
Deriving A2 from reference genome
WARNING: Inferring the alternative allele (A2) from the reference genome. In some instances, there are more than one
alternative allele. Arbitrarily, only the first will be kept. See column `alt_alleles` in your returned sumstats file
for all alternative alleles.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P alt_alleles
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08 C
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08 C
First line of summary statistics file:
MarkerName POS A1 A2 EAF Beta SE Pval
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column
First line of summary statistics file:
SNP BP A1 A2 FRQ BETA SE P
There is no Chromosome or Base Pair Position column found within the data. It must be inferred from other column information.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName A1 A2 EAF Beta SE Pval
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column
First line of summary statistics file:
SNP A1 A2 FRQ BETA SE P
There is no Chromosome or Base Pair Position column found within the data. It must be inferred from other column information.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
1 SNP IDs are not correctly formatted. These will be corrected from the reference genome.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName A1 A2 EAF Beta SE Pval
1 SNP IDs appear to be made up of chr:bp, these will be replaced by their SNP ID from the reference genome
1 SNP IDs are not correctly formatted and will be removed
Summary statistics file does not have obvious CHR/BP columns. Checking to see if they are joined in another column
First line of summary statistics file:
SNP A1 A2 FRQ BETA SE P
There is no Chromosome or Base Pair Position column found within the data. It must be inferred from other column information.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
1 SNP IDs are not correctly formatted. These will be corrected from the reference genome.
1 SNP IDs appear to be made up of chr:bp, these will be replaced by their SNP ID from the reference genome
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
CHR POS A1 A2 EAF Beta SE Pval
There is no SNP column found within the data. It must be inferred from other column information.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
1 SNPs are not on the reference genome. These will be corrected from the reference genome.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
3 SNPs are on chromosomes X, Y, MT and will be removed
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF SE Pval
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
There are existing p-values as low as 5e-324 which LDSC/MAGMA may not be able to handle. These will be converted to 0.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
WARNING: GWAS sumstat file has space field separators instead of tabs (unusual, not proper input for MAGMA).
Temp file with corrected FS created and used instead.
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs12646808 4 3249828 T C 0.6418 0.016 0.003 4.002e-08
rs301800 1 8490603 T C 0.1791 0.019 0.003 1.794e-08
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE Pval
8 SNPs are strand-ambiguous alleles including 4 A/T and 4 C/G ambiguous SNPs. These will be removed
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 FRQ BETA SE P
rs10061788 5 87934707 A G 0.2164 0.021 0.004 2.464e-09
rs1007883 16 51163406 T C 0.3713 -0.015 0.003 5.326e-08
VCF format detected, this will be converted to a standard summary statistics file format.
Inputted VCF format has -log10 P-values, these will be converted to unadjusted p-values in the 'P' column.
First line of summary statistics file:
CHROM POS REF ALT INFO ES SE LP AF ID P
Reordering so first three column headers are SNP, CHR and BP in this order.
Succesfully finished preparing sumstats file, preview:
SNP CHR BP A1 A2 INFO BETA SE LP AF P
rs58108140 1 10583 G A 0.1589 0.0312 0.0393 0.369267 0.1589 0.427300105456596
rs806731 1 30923 G T 0.7843 -0.0114 0.0353 0.126854 0.7843 0.746699739815279
First line of summary statistics file:
MarkerName CHR POS A1 A2 EAF Beta SE
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 48 ]
>
> proc.time()
user system elapsed
190.17 17.50 215.39
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MungeSumstats.Rcheck/examples_i386/MungeSumstats-Ex.timings
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MungeSumstats.Rcheck/examples_x64/MungeSumstats-Ex.timings
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