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SNPRelate.Rcheck/tests_i386/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
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> BiocGenerics:::testPackage("SNPRelate")
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Genetic Relationship Matrix (GRM, GCTA):
Excluding 8,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 1,000
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 282597
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:30:50 2020 (internal increment: 11612)
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Saving to the GDS file:
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Sat Oct 17 08:30:51 2020 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 7,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 2,000
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 559412
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:30:51 2020 (internal increment: 11612)
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Saving to the GDS file:
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Sat Oct 17 08:30:52 2020 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 3,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1066957
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:30:52 2020 (internal increment: 11612)
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Saving to the GDS file:
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Sat Oct 17 08:30:53 2020 Done.
GRM merging:
open 'tmp1.gds' (1,000 variants)
open 'tmp2.gds' (2,000 variants)
open 'tmp3.gds' (3,800 variants)
Weight: 0.147059, 0.294118, 0.558824
Output: tmp.gds
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Genetic Relationship Matrix (GRM, GCTA):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 6,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:30:53 2020 (internal increment: 11612)
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Sat Oct 17 08:30:54 2020 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 8,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 1,000
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 282597
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:30:54 2020 (internal increment: 65536)
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Saving to the GDS file:
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Sat Oct 17 08:30:55 2020 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 7,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 2,000
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 559412
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:30:55 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
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Sat Oct 17 08:30:56 2020 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 5,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 3,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1066957
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:30:56 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
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Saving to the GDS file:
[..................................................] 0%, ETC: ---
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Sat Oct 17 08:30:56 2020 Done.
GRM merging:
open 'tmp1.gds' (1,000 variants)
open 'tmp2.gds' (2,000 variants)
open 'tmp3.gds' (3,800 variants)
Weight: 0.147059, 0.294118, 0.558824
Output: tmp.gds
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Writing ...
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Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 6,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:30:57 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
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Sat Oct 17 08:30:57 2020 Done.
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 1,000
using 1 thread
method: covariance
LD matrix: the sum of all selected genotypes (0,1,2) = 283058
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 1,000
using 1 thread
method: correlation
LD matrix: the sum of all selected genotypes (0,1,2) = 283058
FUNCTION: SNPGDSFileClass
FUNCTION: SNPRelate-package
Start file conversion from PLINK BED to SNP GDS ...
BED file: "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/plinkhapmap.bed.gz"
SNP-major mode (Sample X SNP), 45.7K
FAM file: "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/plinkhapmap.fam.gz"
BIM file: "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/plinkhapmap.bim.gz"
Sat Oct 17 08:31:01 2020 (store sample id, snp id, position, and chromosome)
start writing: 60 samples, 5000 SNPs ...
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Sat Oct 17 08:31:01 2020 Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'HapMap.gds' (98.1K)
# of fragments: 38
save to 'HapMap.gds.tmp'
rename 'HapMap.gds.tmp' (97.8K, reduced: 240B)
# of fragments: 18
Principal Component Analysis (PCA) on genotypes:
Excluding 203 SNPs on non-autosomes
Excluding 28 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 60
# of SNPs: 4,769
using 1 thread
# of principal components: 32
PCA: the sum of all selected genotypes (0,1,2) = 124273
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:01 2020 (internal increment: 53996)
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Sat Oct 17 08:31:02 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:31:02 2020 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
PLINK IBD: the sum of all selected genotypes (0,1,2) = 2446510
Sat Oct 17 08:31:02 2020 (internal increment: 65536)
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Sat Oct 17 08:31:02 2020 Done.
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Sat Oct 17 08:31:03 2020 (internal increment: 65536)
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Sat Oct 17 08:31:03 2020 Done.
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 200
using 1 thread
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 55417
FUNCTION: hapmap_geno
FUNCTION: snpgdsAdmixPlot
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:03 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Sat Oct 17 08:31:04 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:31:04 2020 Done.
FUNCTION: snpgdsAdmixProp
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:04 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:04 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:31:04 2020 Done.
FUNCTION: snpgdsAlleleSwitch
Strand-switching at 50 SNP locus/loci.
Unable to determine switching at 10 SNP locus/loci.
FUNCTION: snpgdsApartSelection
Sat Oct 17 08:31:05 2020 Chromosome 1, # of SNPs: 367
Sat Oct 17 08:31:05 2020 Chromosome 2, # of SNPs: 367
Sat Oct 17 08:31:05 2020 Chromosome 3, # of SNPs: 317
Sat Oct 17 08:31:05 2020 Chromosome 4, # of SNPs: 295
Sat Oct 17 08:31:05 2020 Chromosome 5, # of SNPs: 295
Sat Oct 17 08:31:05 2020 Chromosome 6, # of SNPs: 283
Sat Oct 17 08:31:05 2020 Chromosome 7, # of SNPs: 245
Sat Oct 17 08:31:05 2020 Chromosome 8, # of SNPs: 234
Sat Oct 17 08:31:05 2020 Chromosome 9, # of SNPs: 202
Sat Oct 17 08:31:05 2020 Chromosome 10, # of SNPs: 224
Sat Oct 17 08:31:05 2020 Chromosome 11, # of SNPs: 223
Sat Oct 17 08:31:05 2020 Chromosome 12, # of SNPs: 208
Sat Oct 17 08:31:05 2020 Chromosome 13, # of SNPs: 172
Sat Oct 17 08:31:05 2020 Chromosome 14, # of SNPs: 147
Sat Oct 17 08:31:05 2020 Chromosome 15, # of SNPs: 121
Sat Oct 17 08:31:05 2020 Chromosome 16, # of SNPs: 129
Sat Oct 17 08:31:05 2020 Chromosome 17, # of SNPs: 116
Sat Oct 17 08:31:05 2020 Chromosome 18, # of SNPs: 129
Sat Oct 17 08:31:05 2020 Chromosome 19, # of SNPs: 73
Sat Oct 17 08:31:05 2020 Chromosome 20, # of SNPs: 106
Sat Oct 17 08:31:05 2020 Chromosome 21, # of SNPs: 62
Sat Oct 17 08:31:05 2020 Chromosome 22, # of SNPs: 51
Sat Oct 17 08:31:05 2020 Chromosome 23, # of SNPs: 204
Total # of SNPs selected:4570
FUNCTION: snpgdsBED2GDS
Start file conversion from PLINK BED to SNP GDS ...
BED file: "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/plinkhapmap.bed.gz"
SNP-major mode (Sample X SNP), 45.7K
FAM file: "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/plinkhapmap.fam.gz"
BIM file: "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/plinkhapmap.bim.gz"
Sat Oct 17 08:31:05 2020 (store sample id, snp id, position, and chromosome)
start writing: 60 samples, 5000 SNPs ...
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:05 2020 Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'HapMap.gds' (98.1K)
# of fragments: 38
save to 'HapMap.gds.tmp'
rename 'HapMap.gds.tmp' (97.8K, reduced: 240B)
# of fragments: 18
FUNCTION: snpgdsClose
FUNCTION: snpgdsCombineGeno
Create a GDS genotype file:
The new dataset consists of 10 samples and 3000 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Create a GDS genotype file:
The new dataset consists of 20 samples and 3000 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Merge SNP GDS files:
open 't1.gds' ...
10 samples, 3000 SNPs
open 't2.gds' ...
20 samples, 3000 SNPs
Concatenating samples (mapping to the first GDS file) ...
reference: 3000 SNPs (100.0%)
file 2: 0 allele flips, 0 ambiguous locus/loci
[no flip]: 3000
create 'test.gds': 30 samples, 3000 SNPs
FileFormat = SNP_ARRAY
writing genotypes ...
Clean up the fragments of GDS file:
open the file 'test.gds' (46.2K)
# of fragments: 32
save to 'test.gds.tmp'
rename 'test.gds.tmp' (46.0K, reduced: 204B)
# of fragments: 15
Done.
Create a GDS genotype file:
The new dataset consists of 279 samples and 100 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Create a GDS genotype file:
The new dataset consists of 279 samples and 200 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Merge SNP GDS files:
open 't1.gds' ...
279 samples, 100 SNPs
open 't2.gds' ...
279 samples, 200 SNPs
Concatenating SNPs ...
create 'test.gds': 279 samples, 300 SNPs
FileFormat = SNP_ARRAY
writing genotypes ...
Clean up the fragments of GDS file:
open the file 'test.gds' (19.1K)
# of fragments: 32
save to 'test.gds.tmp'
rename 'test.gds.tmp' (18.9K, reduced: 204B)
# of fragments: 15
Done.
FUNCTION: snpgdsCreateGeno
Principal Component Analysis (PCA) on genotypes:
Excluding 42 SNPs on non-autosomes
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 958
using 1 thread
# of principal components: 32
PCA: the sum of all selected genotypes (0,1,2) = 264760
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:05 2020 (internal increment: 11612)
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[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:05 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:31:05 2020 Done.
FUNCTION: snpgdsCreateGenoSet
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 76.12%, 545/716
Chromosome 2: 72.78%, 540/742
Chromosome 3: 74.71%, 455/609
Chromosome 4: 73.49%, 413/562
Chromosome 5: 76.86%, 435/566
Chromosome 6: 75.75%, 428/565
Chromosome 7: 75.42%, 356/472
Chromosome 8: 71.11%, 347/488
Chromosome 9: 77.88%, 324/416
Chromosome 10: 74.12%, 358/483
Chromosome 11: 77.85%, 348/447
Chromosome 12: 76.81%, 328/427
Chromosome 13: 76.16%, 262/344
Chromosome 14: 76.60%, 216/282
Chromosome 15: 76.34%, 200/262
Chromosome 16: 72.66%, 202/278
Chromosome 17: 73.91%, 153/207
Chromosome 18: 73.68%, 196/266
Chromosome 19: 85.00%, 102/120
Chromosome 20: 71.62%, 164/229
Chromosome 21: 76.98%, 97/126
Chromosome 22: 75.86%, 88/116
6,557 markers are selected in total.
Create a GDS genotype file:
The new dataset consists of 279 samples and 6557 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
FUNCTION: snpgdsCutTree
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Sat Oct 17 08:31:06 2020 0%
Dissimilarity: Sat Oct 17 08:31:07 2020 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
Create 4 groups.
FUNCTION: snpgdsDiss
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Sat Oct 17 08:31:08 2020 0%
Dissimilarity: Sat Oct 17 08:31:09 2020 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsDrawTree
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Sat Oct 17 08:31:10 2020 0%
Dissimilarity: Sat Oct 17 08:31:11 2020 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsEIGMIX
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:12 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:12 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:31:12 2020 Done.
FUNCTION: snpgdsErrMsg
FUNCTION: snpgdsExampleFileName
FUNCTION: snpgdsFst
Fst estimation on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
Method: Weir & Cockerham, 1984
# of Populations: 4
CEU (92), HCB (47), JPT (47), YRI (93)
Fst estimation on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
Method: Weir & Hill, 2002
# of Populations: 4
CEU (92), HCB (47), JPT (47), YRI (93)
FUNCTION: snpgdsGDS2BED
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: 0.95)
Converting from GDS to PLINK binary PED:
Working space: 279 samples, 8722 SNPs
Output a BIM file.
Output a BED file ...
Sat Oct 17 08:31:12 2020 0%
Sat Oct 17 08:31:12 2020 100%
Done.
FUNCTION: snpgdsGDS2Eigen
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: 0.95)
Converting from GDS to EIGENSOFT:
save to *.snp: 8722 snps
save to *.ind: 279 samples
Output: Sat Oct 17 08:31:12 2020 0%
Output: Sat Oct 17 08:31:12 2020 100%
Done.
FUNCTION: snpgdsGDS2PED
Converting from GDS to PLINK PED:
Output a MAP file DONE.
Output a PED file ...
Output: Sat Oct 17 08:31:12 2020 0%
Output: Sat Oct 17 08:31:13 2020 100%
FUNCTION: snpgdsGEN2GDS
running snpgdsGEN2GDS ...
FUNCTION: snpgdsGRM
Genetic Relationship Matrix (GRM, GCTA):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:13 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:13 2020 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:13 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:14 2020 Done.
FUNCTION: snpgdsGetGeno
Genotype matrix: 1000 SNPs X 279 samples
Genotype matrix: 279 samples X 1000 SNPs
FUNCTION: snpgdsHCluster
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Sat Oct 17 08:31:14 2020 0%
Dissimilarity: Sat Oct 17 08:31:15 2020 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsHWE
Keeping 716 SNPs according to chromosome 1
Excluding 160 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
FUNCTION: snpgdsIBDKING
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
No family is specified, and all individuals are treated as singletons.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:16 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:16 2020 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
No family is specified, and all individuals are treated as singletons.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:16 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:16 2020 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
# of families: 20, and within- and between-family relationship are estimated differently.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:17 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Sat Oct 17 08:31:18 2020 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
Relationship inference in a homogeneous population.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
Sat Oct 17 08:31:18 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:18 2020 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
Relationship inference in a homogeneous population.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
Sat Oct 17 08:31:18 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:18 2020 Done.
FUNCTION: snpgdsIBDMLE
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,581 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
# of samples: 30
# of SNPs: 7,142
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 54.75%, 392/716
Chromosome 2: 54.31%, 403/742
Chromosome 3: 55.99%, 341/609
Chromosome 4: 56.58%, 318/562
Chromosome 5: 56.36%, 319/566
Chromosome 6: 52.74%, 298/565
Chromosome 7: 56.14%, 265/472
Chromosome 8: 51.84%, 253/488
Chromosome 9: 54.81%, 228/416
Chromosome 10: 49.90%, 241/483
Chromosome 11: 54.81%, 245/447
Chromosome 12: 54.57%, 233/427
Chromosome 13: 53.49%, 184/344
Chromosome 14: 56.03%, 158/282
Chromosome 15: 54.58%, 143/262
Chromosome 16: 54.68%, 152/278
Chromosome 17: 55.56%, 115/207
Chromosome 18: 55.64%, 148/266
Chromosome 19: 66.67%, 80/120
Chromosome 20: 53.28%, 122/229
Chromosome 21: 50.79%, 64/126
Chromosome 22: 51.72%, 60/116
4,762 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 30
# of SNPs: 250
using 1 thread
MLE IBD: the sum of all selected genotypes (0,1,2) = 7859
MLE IBD: Sat Oct 17 08:31:18 2020 0%
MLE IBD: Sat Oct 17 08:31:19 2020 100%
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.525, sd: 0.288
MLE IBD: the sum of all selected genotypes (0,1,2) = 6545
MLE IBD: Sat Oct 17 08:31:19 2020 0%
MLE IBD: Sat Oct 17 08:31:19 2020 100%
FUNCTION: snpgdsIBDMLELogLik
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,581 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
# of samples: 30
# of SNPs: 7,142
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 54.75%, 392/716
Chromosome 2: 54.31%, 403/742
Chromosome 3: 55.99%, 341/609
Chromosome 4: 56.58%, 318/562
Chromosome 5: 56.36%, 319/566
Chromosome 6: 52.74%, 298/565
Chromosome 7: 56.14%, 265/472
Chromosome 8: 51.84%, 253/488
Chromosome 9: 54.81%, 228/416
Chromosome 10: 49.90%, 241/483
Chromosome 11: 54.81%, 245/447
Chromosome 12: 54.57%, 233/427
Chromosome 13: 53.49%, 184/344
Chromosome 14: 56.03%, 158/282
Chromosome 15: 54.58%, 143/262
Chromosome 16: 54.68%, 152/278
Chromosome 17: 55.56%, 115/207
Chromosome 18: 55.64%, 148/266
Chromosome 19: 66.67%, 80/120
Chromosome 20: 53.28%, 122/229
Chromosome 21: 50.79%, 64/126
Chromosome 22: 51.72%, 60/116
4,762 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 30
# of SNPs: 250
using 1 thread
MLE IBD: the sum of all selected genotypes (0,1,2) = 7859
MLE IBD: Sat Oct 17 08:31:19 2020 0%
MLE IBD: Sat Oct 17 08:31:21 2020 100%
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.525, sd: 0.288
MLE IBD: the sum of all selected genotypes (0,1,2) = 6545
MLE IBD: Sat Oct 17 08:31:21 2020 0%
MLE IBD: Sat Oct 17 08:31:21 2020 100%
FUNCTION: snpgdsIBDMoM
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
PLINK IBD: the sum of all selected genotypes (0,1,2) = 702139
Sat Oct 17 08:31:21 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:21 2020 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 93
# of SNPs: 8,160
using 1 thread
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Sat Oct 17 08:31:21 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:21 2020 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 93
# of SNPs: 8,160
using 1 thread
Specifying allele frequencies, mean: 0.500, sd: 0.315
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Sat Oct 17 08:31:21 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:21 2020 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 8,160
using 1 thread
Specifying allele frequencies, mean: 0.500, sd: 0.315
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 203285
Sat Oct 17 08:31:21 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:21 2020 Done.
FUNCTION: snpgdsIBDSelection
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 93
# of SNPs: 8,160
using 1 thread
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Sat Oct 17 08:31:21 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:21 2020 Done.
FUNCTION: snpgdsIBS
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Sat Oct 17 08:31:22 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:22 2020 Done.
FUNCTION: snpgdsIBSNum
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Sat Oct 17 08:31:22 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:22 2020 Done.
FUNCTION: snpgdsIndInb
Estimating individual inbreeding coefficients:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
FUNCTION: snpgdsIndInbCoef
FUNCTION: snpgdsIndivBeta
Individual Inbreeding and Relatedness (beta estimator):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Individual Beta: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:23 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:23 2020 Done.
FUNCTION: snpgdsLDMat
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 203
using 1 thread
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 56582
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 203
using 1 thread
sliding window size: 203
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 56582
FUNCTION: snpgdsLDpair
FUNCTION: snpgdsLDpruning
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 76.12%, 545/716
Chromosome 2: 72.78%, 540/742
Chromosome 3: 74.71%, 455/609
Chromosome 4: 73.49%, 413/562
Chromosome 5: 76.86%, 435/566
Chromosome 6: 75.75%, 428/565
Chromosome 7: 75.42%, 356/472
Chromosome 8: 71.11%, 347/488
Chromosome 9: 77.88%, 324/416
Chromosome 10: 74.12%, 358/483
Chromosome 11: 77.85%, 348/447
Chromosome 12: 76.81%, 328/427
Chromosome 13: 76.16%, 262/344
Chromosome 14: 76.60%, 216/282
Chromosome 15: 76.34%, 200/262
Chromosome 16: 72.66%, 202/278
Chromosome 17: 73.91%, 153/207
Chromosome 18: 73.68%, 196/266
Chromosome 19: 85.00%, 102/120
Chromosome 20: 71.62%, 164/229
Chromosome 21: 76.98%, 97/126
Chromosome 22: 75.86%, 88/116
6,557 markers are selected in total.
List of 22
$ chr1 : int [1:545] 1 2 4 5 7 10 12 14 15 16 ...
$ chr2 : int [1:540] 717 718 719 720 721 723 724 725 726 727 ...
$ chr3 : int [1:455] 1459 1460 1461 1464 1466 1468 1469 1471 1472 1473 ...
$ chr4 : int [1:413] 2068 2069 2070 2071 2072 2074 2075 2076 2077 2078 ...
$ chr5 : int [1:435] 2630 2631 2633 2635 2636 2637 2638 2640 2642 2643 ...
$ chr6 : int [1:428] 3196 3197 3198 3200 3201 3204 3205 3206 3207 3208 ...
$ chr7 : int [1:356] 3761 3762 3763 3766 3767 3768 3770 3771 3772 3773 ...
$ chr8 : int [1:347] 4233 4234 4235 4236 4237 4238 4239 4240 4241 4242 ...
$ chr9 : int [1:324] 4721 4722 4724 4727 4728 4730 4731 4732 4733 4735 ...
$ chr10: int [1:358] 5138 5139 5140 5143 5144 5145 5146 5147 5148 5149 ...
$ chr11: int [1:348] 5620 5621 5623 5624 5625 5626 5628 5629 5630 5631 ...
$ chr12: int [1:328] 6067 6068 6069 6070 6073 6074 6075 6077 6078 6079 ...
$ chr13: int [1:262] 6494 6497 6498 6499 6500 6501 6503 6505 6507 6509 ...
$ chr14: int [1:216] 6840 6841 6842 6843 6844 6845 6846 6847 6848 6850 ...
$ chr15: int [1:200] 7120 7121 7122 7124 7125 7126 7127 7128 7129 7130 ...
$ chr16: int [1:202] 7382 7383 7384 7385 7387 7388 7389 7391 7392 7394 ...
$ chr17: int [1:153] 7660 7661 7662 7663 7664 7665 7666 7667 7668 7669 ...
$ chr18: int [1:196] 7867 7868 7869 7870 7871 7872 7873 7874 7875 7877 ...
$ chr19: int [1:102] 8133 8135 8136 8137 8138 8139 8140 8141 8142 8144 ...
$ chr20: int [1:164] 8253 8254 8257 8258 8259 8260 8261 8262 8265 8266 ...
$ chr21: int [1:97] 8482 8484 8485 8486 8487 8488 8489 8490 8491 8492 ...
$ chr22: int [1:88] 8608 8609 8610 8612 8613 8614 8615 8617 8618 8619 ...
FUNCTION: snpgdsMergeGRM
Genetic Relationship Matrix (GRM, GCTA):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 6,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:24 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:24 2020 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,688 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 3,400
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 951558
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:24 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:25 2020 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,688 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 3,400
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 957408
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:25 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:25 2020 Done.
GRM merging:
open 'tmp1.gds' (3,400 variants)
open 'tmp2.gds' (3,400 variants)
Weight: 0.5, 0.5
Output: tmp.gds
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
GRM merging:
open 'tmp1.gds' (3,400 variants)
open 'tmp2.gds' (3,400 variants)
Weight: 0.5, 0.5
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
FUNCTION: snpgdsOpen
FUNCTION: snpgdsOption
FUNCTION: snpgdsPCA
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
# of principal components: 32
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:26 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:26 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:31:26 2020 Done.
FUNCTION: snpgdsPCACorr
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
# of principal components: 32
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:27 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:27 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:31:27 2020 Done.
SNP Correlation:
# of samples: 279
# of SNPs: 9,088
using 1 thread
Correlation: the sum of all selected genotypes (0,1,2) = 2553065
Sat Oct 17 08:31:27 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:27 2020 Done.
SNP Correlation:
# of samples: 279
# of SNPs: 9,088
using 1 thread
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 2553065
Sat Oct 17 08:31:27 2020
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:27 2020 Done.
FUNCTION: snpgdsPCASNPLoading
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
# of principal components: 8
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:27 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Sat Oct 17 08:31:28 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:31:28 2020 Done.
SNP Loading:
# of samples: 279
# of SNPs: 8,722
using 1 thread
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 2446510
Sat Oct 17 08:31:28 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:28 2020 Done.
FUNCTION: snpgdsPCASampLoading
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
# of principal components: 8
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:28 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:28 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:31:28 2020 Done.
SNP Loading:
# of samples: 279
# of SNPs: 8,722
using 1 thread
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 2446510
Sat Oct 17 08:31:29 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:29 2020 Done.
Sample Loading:
# of samples: 100
# of SNPs: 8,722
using 1 thread
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 878146
Sat Oct 17 08:31:29 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:29 2020 Done.
FUNCTION: snpgdsPED2GDS
Converting from GDS to PLINK PED:
Output a MAP file DONE.
Output a PED file ...
Output: Sat Oct 17 08:31:29 2020 0%
Output: Sat Oct 17 08:31:29 2020 100%
PLINK PED/MAP to GDS Format:
Import 9088 variants from 'tmp.map'
Chromosome:
1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7
716 483 447 427 344 282 262 278 207 266 120 742 229 126 116 609 562 566 565 472
8 9 X
488 416 365
Reading 'tmp.ped'
Output: 'test.gds'
Import 279 samples
Transpose the genotypic matrix ...
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test.gds' (1.3M)
# of fragments: 50
save to 'test.gds.tmp'
rename 'test.gds.tmp' (711.4K, reduced: 618.7K)
# of fragments: 26
FUNCTION: snpgdsPairIBD
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,646 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
# of samples: 93
# of SNPs: 7,077
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 62.29%, 446/716
Chromosome 2: 62.67%, 465/742
Chromosome 3: 59.93%, 365/609
Chromosome 4: 64.23%, 361/562
Chromosome 5: 62.37%, 353/566
Chromosome 6: 59.82%, 338/565
Chromosome 7: 63.14%, 298/472
Chromosome 8: 57.58%, 281/488
Chromosome 9: 62.98%, 262/416
Chromosome 10: 60.46%, 292/483
Chromosome 11: 63.09%, 282/447
Chromosome 12: 62.76%, 268/427
Chromosome 13: 63.08%, 217/344
Chromosome 14: 63.83%, 180/282
Chromosome 15: 63.74%, 167/262
Chromosome 16: 62.23%, 173/278
Chromosome 17: 65.70%, 136/207
Chromosome 18: 59.40%, 158/266
Chromosome 19: 68.33%, 82/120
Chromosome 20: 66.38%, 152/229
Chromosome 21: 61.11%, 77/126
Chromosome 22: 57.76%, 67/116
5,420 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
MLE IBD: the sum of all selected genotypes (0,1,2) = 6112
MLE IBD: Sat Oct 17 08:31:30 2020 0%
MLE IBD: Sat Oct 17 08:31:31 2020 100%
IBD analysis (PLINK method of moment) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 6112
Sat Oct 17 08:31:31 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:31 2020 Done.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
MLE IBD: the sum of all selected genotypes (0,1,2) = 6112
MLE IBD: Sat Oct 17 08:31:31 2020 0%
MLE IBD: Sat Oct 17 08:31:32 2020 100%
Genotype matrix: 250 SNPs X 25 samples
[1] -370.7482
[1] -402.2141
[1] -383.7897
[1] -377.9084
[1] -381.3139
[1] -397.5581
[1] -378.3344
[1] -370.703
[1] -376.103
[1] -377.7911
[1] -375.5425
[1] -373.13
[1] -383.6992
[1] -393.5194
[1] -371.9843
[1] -369.6468
[1] -374.5139
[1] -377.841
[1] -387.5622
[1] -377.1646
[1] -377.4659
[1] -375.2204
[1] -372.0639
[1] -379.816
FUNCTION: snpgdsPairIBDMLELogLik
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,646 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
# of samples: 93
# of SNPs: 7,077
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 62.29%, 446/716
Chromosome 2: 62.67%, 465/742
Chromosome 3: 59.93%, 365/609
Chromosome 4: 64.23%, 361/562
Chromosome 5: 62.37%, 353/566
Chromosome 6: 59.82%, 338/565
Chromosome 7: 63.14%, 298/472
Chromosome 8: 57.58%, 281/488
Chromosome 9: 62.98%, 262/416
Chromosome 10: 60.46%, 292/483
Chromosome 11: 63.09%, 282/447
Chromosome 12: 62.76%, 268/427
Chromosome 13: 63.08%, 217/344
Chromosome 14: 63.83%, 180/282
Chromosome 15: 63.74%, 167/262
Chromosome 16: 62.23%, 173/278
Chromosome 17: 65.70%, 136/207
Chromosome 18: 59.40%, 158/266
Chromosome 19: 68.33%, 82/120
Chromosome 20: 66.38%, 152/229
Chromosome 21: 61.11%, 77/126
Chromosome 22: 57.76%, 67/116
5,420 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
MLE IBD: the sum of all selected genotypes (0,1,2) = 6112
MLE IBD: Sat Oct 17 08:31:32 2020 0%
MLE IBD: Sat Oct 17 08:31:33 2020 100%
IBD analysis (PLINK method of moment) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 6112
Sat Oct 17 08:31:33 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:33 2020 Done.
Genotype matrix: 250 SNPs X 25 samples
[1] -370.7482
[1] -402.2141
[1] -383.7897
[1] -377.9084
[1] -381.3139
[1] -397.5581
[1] -378.3344
[1] -370.703
[1] -376.103
[1] -377.7911
[1] -375.5425
[1] -373.13
[1] -383.6992
[1] -393.5194
[1] -371.9843
[1] -369.6468
[1] -374.5139
[1] -377.841
[1] -387.5622
[1] -377.1646
[1] -377.4659
[1] -375.2204
[1] -372.0639
[1] -379.816
FUNCTION: snpgdsPairScore
Excluding 365 SNPs on non-autosomes
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
List of 3
$ sample.id: chr [1:120] "NA19139" "NA19160" "NA07034" "NA12814" ...
$ snp.id : int [1:8723] 1 2 3 4 5 6 7 8 9 10 ...
$ score :'data.frame': 60 obs. of 5 variables:
..$ Avg : num [1:60] 1.72 1.73 1.71 1.72 1.73 ...
..$ SD : num [1:60] 0.452 0.443 0.457 0.45 0.443 ...
..$ Num : int [1:60] 8684 8627 8669 8637 8682 8634 8654 8678 8680 8679 ...
..$ Sample1: chr [1:60] "NA19139" "NA10847" "NA18515" "NA19129" ...
..$ Sample2: chr [1:60] "NA19138" "NA12146" "NA18516" "NA19128" ...
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
List of 3
$ sample.id: chr [1:120] "NA19139" "NA19160" "NA07034" "NA12814" ...
$ snp.id : int [1:8723] 1 2 3 4 5 6 7 8 9 10 ...
$ score :'data.frame': 60 obs. of 5 variables:
..$ Avg : num [1:60] 0.999 1 1 1 1 ...
..$ SD : num [1:60] 0.024 0 0.0186 0.0215 0.0215 ...
..$ Num : int [1:60] 8684 8627 8669 8637 8682 8634 8654 8678 8680 8679 ...
..$ Sample1: chr [1:60] "NA19139" "NA10847" "NA18515" "NA19129" ...
..$ Sample2: chr [1:60] "NA19138" "NA12146" "NA18516" "NA19128" ...
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
List of 3
$ sample.id: chr [1:120] "NA19139" "NA19160" "NA07034" "NA12814" ...
$ snp.id : int [1:8723] 1 2 3 4 5 6 7 8 9 10 ...
$ score : num [1:3, 1:8723] 1.75 0.437 60 1.583 0.497 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:3] "Avg" "SD" "Num"
.. ..$ : NULL
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
List of 3
$ sample.id: chr [1:120] "NA19139" "NA19160" "NA07034" "NA12814" ...
$ snp.id : int [1:8723] 1 2 3 4 5 6 7 8 9 10 ...
$ score : int [1:60, 1:8723] 1 1 2 2 2 2 2 1 2 2 ...
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Output: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_i386\tmp.gds
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
FUNCTION: snpgdsSNPList
FUNCTION: snpgdsSNPListClass
FUNCTION: snpgdsSNPListIntersect
FUNCTION: snpgdsSNPRateFreq
FUNCTION: snpgdsSampMissRate
FUNCTION: snpgdsSelectSNP
Excluding 365 SNPs on non-autosomes
Excluding 1,221 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.95)
FUNCTION: snpgdsSlidingWindow
Sliding Window Analysis:
Excluding 8 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 9,080
using 1 thread
window size: 500000, shift: 100000 (basepair)
Chromosome Set: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23
Sat Oct 17 08:31:34 2020, Chromosome 1 (716 SNPs), 2448 windows
Sat Oct 17 08:31:34 2020, Chromosome 2 (742 SNPs), 2416 windows
Sat Oct 17 08:31:34 2020, Chromosome 3 (609 SNPs), 1985 windows
Sat Oct 17 08:31:34 2020, Chromosome 4 (562 SNPs), 1894 windows
Sat Oct 17 08:31:34 2020, Chromosome 5 (566 SNPs), 1797 windows
Sat Oct 17 08:31:34 2020, Chromosome 6 (565 SNPs), 1694 windows
Sat Oct 17 08:31:34 2020, Chromosome 7 (472 SNPs), 1573 windows
Sat Oct 17 08:31:34 2020, Chromosome 8 (488 SNPs), 1445 windows
Sat Oct 17 08:31:34 2020, Chromosome 9 (416 SNPs), 1393 windows
Sat Oct 17 08:31:34 2020, Chromosome 10 (483 SNPs), 1343 windows
Sat Oct 17 08:31:34 2020, Chromosome 11 (447 SNPs), 1338 windows
Sat Oct 17 08:31:35 2020, Chromosome 12 (427 SNPs), 1316 windows
Sat Oct 17 08:31:35 2020, Chromosome 13 (344 SNPs), 948 windows
Sat Oct 17 08:31:35 2020, Chromosome 14 (281 SNPs), 847 windows
Sat Oct 17 08:31:35 2020, Chromosome 15 (262 SNPs), 774 windows
Sat Oct 17 08:31:35 2020, Chromosome 16 (278 SNPs), 873 windows
Sat Oct 17 08:31:35 2020, Chromosome 17 (207 SNPs), 773 windows
Sat Oct 17 08:31:35 2020, Chromosome 18 (266 SNPs), 753 windows
Sat Oct 17 08:31:35 2020, Chromosome 19 (120 SNPs), 627 windows
Sat Oct 17 08:31:35 2020, Chromosome 20 (229 SNPs), 602 windows
Sat Oct 17 08:31:35 2020, Chromosome 21 (126 SNPs), 311 windows
Sat Oct 17 08:31:35 2020, Chromosome 22 (116 SNPs), 312 windows
Sat Oct 17 08:31:35 2020, Chromosome 23 (358 SNPs), 1507 windows
Sat Oct 17 08:31:35 2020 Done.
FUNCTION: snpgdsSummary
The file name: C:\Users\biocbuild\bbs-3.11-bioc\R\library\SNPRelate\extdata\hapmap_geno.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in SNP-major mode (Sample X SNP).
FUNCTION: snpgdsTranspose
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_i386\test.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in SNP-major mode (Sample X SNP).
SNP genotypes: 279 samples, 9088 SNPs
Genotype matrix is being transposed ...
Clean up the fragments of GDS file:
open the file 'test.gds' (1.3M)
# of fragments: 28
save to 'test.gds.tmp'
rename 'test.gds.tmp' (709.6K, reduced: 619.1K)
# of fragments: 26
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_i386\test.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in individual-major mode (SNP X Sample).
FUNCTION: snpgdsVCF2GDS
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
Start file conversion from VCF to SNP GDS ...
Method: exacting biallelic SNPs
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 2 variants.
+ genotype { Bit2 3x2, 2B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test1.gds' (2.9K)
# of fragments: 46
save to 'test1.gds.tmp'
rename 'test1.gds.tmp' (2.6K, reduced: 312B)
# of fragments: 20
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_i386\test1.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start file conversion from VCF to SNP GDS ...
Method: exacting biallelic SNPs
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 2 variants.
+ genotype { Bit2 3x2, 2B } *
SNP genotypes: 3 samples, 2 SNPs
Genotype matrix is being transposed ...
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test2.gds' (3.0K)
# of fragments: 48
save to 'test2.gds.tmp'
rename 'test2.gds.tmp' (2.6K, reduced: 417B)
# of fragments: 20
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_i386\test2.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in individual-major mode (SNP X Sample).
Start file conversion from VCF to SNP GDS ...
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
SNP genotypes: 3 samples, 5 SNPs
Genotype matrix is being transposed ...
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test3.gds' (3.1K)
# of fragments: 48
save to 'test3.gds.tmp'
rename 'test3.gds.tmp' (2.7K, reduced: 419B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_i386\test3.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in individual-major mode (SNP X Sample).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
Start file conversion from VCF to SNP GDS ...
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test4.gds' (3.0K)
# of fragments: 46
save to 'test4.gds.tmp'
rename 'test4.gds.tmp' (2.7K, reduced: 312B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_i386\test4.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
Start file conversion from VCF to SNP GDS ...
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test5.gds' (3.0K)
# of fragments: 46
save to 'test5.gds.tmp'
rename 'test5.gds.tmp' (2.7K, reduced: 312B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., T/A,G).
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_i386\test5.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
FUNCTION: snpgdsVCF2GDS_R
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
Start snpgdsVCF2GDS ...
Extracting bi-allelic and polymorhpic SNPs.
Scanning ...
file: C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Sat Oct 17 08:31:35 2020 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 2 SNPs ...
file: C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf
[1] 1
Sat Oct 17 08:31:35 2020 Done.
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_i386\test1.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start snpgdsVCF2GDS ...
Extracting bi-allelic and polymorhpic SNPs.
Scanning ...
file: C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Sat Oct 17 08:31:35 2020 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 2 SNPs ...
file: C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf
[1] 1
Sat Oct 17 08:31:35 2020 Done.
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_i386\test2.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start snpgdsVCF2GDS ...
Storing dosage of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants.
Scanning ...
file: C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Sat Oct 17 08:31:35 2020 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 5 SNPs ...
file: C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf
Sat Oct 17 08:31:35 2020 Done.
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_i386\test3.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
Start snpgdsVCF2GDS ...
Storing dosage of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants.
Scanning ...
file: C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Sat Oct 17 08:31:35 2020 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 5 SNPs ...
file: C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf
Sat Oct 17 08:31:35 2020 Done.
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_i386\test4.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
SNP Correlation:
# of samples: 90
# of SNPs: 9,088
using 1 thread
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Sat Oct 17 08:31:37 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:37 2020 Done.
SNP Correlation:
# of samples: 90
# of SNPs: 9,088
using 1 thread
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Sat Oct 17 08:31:37 2020
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:37 2020 Done.
SNP Loading:
# of samples: 90
# of SNPs: 8,695
using 1 thread
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 787449
Sat Oct 17 08:31:37 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:37 2020 Done.
Sample Loading:
# of samples: 100
# of SNPs: 8,695
using 1 thread
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 875255
Sat Oct 17 08:31:37 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:37 2020 Done.
SNP Correlation:
# of samples: 90
# of SNPs: 9,088
using 2 threads
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Sat Oct 17 08:31:38 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:38 2020 Done.
SNP Correlation:
# of samples: 90
# of SNPs: 9,088
using 2 threads
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Sat Oct 17 08:31:38 2020
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:38 2020 Done.
SNP Loading:
# of samples: 90
# of SNPs: 8,695
using 1 thread
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 787449
Sat Oct 17 08:31:38 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:38 2020 Done.
Sample Loading:
# of samples: 100
# of SNPs: 8,695
using 1 thread
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 875255
Sat Oct 17 08:31:38 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:38 2020 Done.
RUNIT TEST PROTOCOL -- Sat Oct 17 08:31:38 2020
***********************************************
Number of test functions: 13
Number of errors: 0
Number of failures: 0
1 Test Suite :
SNPRelate RUnit Tests - 13 test functions, 0 errors, 0 failures
Number of test functions: 13
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
46.48 2.35 48.86
|
SNPRelate.Rcheck/tests_x64/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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> BiocGenerics:::testPackage("SNPRelate")
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Genetic Relationship Matrix (GRM, GCTA):
Excluding 8,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 1,000
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 282597
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:40 2020 (internal increment: 11612)
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Saving to the GDS file:
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Sat Oct 17 08:31:41 2020 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 7,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 2,000
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 559412
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:41 2020 (internal increment: 11612)
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Saving to the GDS file:
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Sat Oct 17 08:31:42 2020 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 3,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1066957
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:42 2020 (internal increment: 11612)
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Saving to the GDS file:
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Sat Oct 17 08:31:43 2020 Done.
GRM merging:
open 'tmp1.gds' (1,000 variants)
open 'tmp2.gds' (2,000 variants)
open 'tmp3.gds' (3,800 variants)
Weight: 0.147059, 0.294118, 0.558824
Output: tmp.gds
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Genetic Relationship Matrix (GRM, GCTA):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 6,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:43 2020 (internal increment: 11612)
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Sat Oct 17 08:31:44 2020 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 8,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 1,000
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 282597
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:44 2020 (internal increment: 65536)
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Saving to the GDS file:
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Sat Oct 17 08:31:45 2020 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 7,088 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 2,000
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 559412
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:45 2020 (internal increment: 65536)
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Saving to the GDS file:
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Sat Oct 17 08:31:45 2020 Done.
Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 5,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 3,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1066957
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:45 2020 (internal increment: 65536)
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Saving to the GDS file:
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Sat Oct 17 08:31:46 2020 Done.
GRM merging:
open 'tmp1.gds' (1,000 variants)
open 'tmp2.gds' (2,000 variants)
open 'tmp3.gds' (3,800 variants)
Weight: 0.147059, 0.294118, 0.558824
Output: tmp.gds
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Writing ...
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Genetic Relationship Matrix (GRM, IndivBeta):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 6,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:47 2020 (internal increment: 65536)
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Sat Oct 17 08:31:47 2020 Done.
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 1,000
using 1 thread
method: covariance
LD matrix: the sum of all selected genotypes (0,1,2) = 283058
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 1,000
using 1 thread
method: correlation
LD matrix: the sum of all selected genotypes (0,1,2) = 283058
FUNCTION: SNPGDSFileClass
FUNCTION: SNPRelate-package
Start file conversion from PLINK BED to SNP GDS ...
BED file: "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/plinkhapmap.bed.gz"
SNP-major mode (Sample X SNP), 45.7K
FAM file: "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/plinkhapmap.fam.gz"
BIM file: "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/plinkhapmap.bim.gz"
Sat Oct 17 08:31:51 2020 (store sample id, snp id, position, and chromosome)
start writing: 60 samples, 5000 SNPs ...
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Sat Oct 17 08:31:51 2020 Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'HapMap.gds' (98.1K)
# of fragments: 38
save to 'HapMap.gds.tmp'
rename 'HapMap.gds.tmp' (97.8K, reduced: 240B)
# of fragments: 18
Principal Component Analysis (PCA) on genotypes:
Excluding 203 SNPs on non-autosomes
Excluding 28 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 60
# of SNPs: 4,769
using 1 thread
# of principal components: 32
PCA: the sum of all selected genotypes (0,1,2) = 124273
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:51 2020 (internal increment: 53996)
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Sat Oct 17 08:31:51 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:31:51 2020 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
PLINK IBD: the sum of all selected genotypes (0,1,2) = 2446510
Sat Oct 17 08:31:51 2020 (internal increment: 65536)
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Sat Oct 17 08:31:51 2020 Done.
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Sat Oct 17 08:31:52 2020 (internal increment: 65536)
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Sat Oct 17 08:31:53 2020 Done.
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 200
using 1 thread
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 55417
FUNCTION: hapmap_geno
FUNCTION: snpgdsAdmixPlot
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:53 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Sat Oct 17 08:31:54 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:31:54 2020 Done.
FUNCTION: snpgdsAdmixProp
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:54 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:54 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:31:54 2020 Done.
FUNCTION: snpgdsAlleleSwitch
Strand-switching at 50 SNP locus/loci.
Unable to determine switching at 10 SNP locus/loci.
FUNCTION: snpgdsApartSelection
Sat Oct 17 08:31:55 2020 Chromosome 1, # of SNPs: 367
Sat Oct 17 08:31:55 2020 Chromosome 2, # of SNPs: 367
Sat Oct 17 08:31:55 2020 Chromosome 3, # of SNPs: 317
Sat Oct 17 08:31:55 2020 Chromosome 4, # of SNPs: 295
Sat Oct 17 08:31:55 2020 Chromosome 5, # of SNPs: 295
Sat Oct 17 08:31:55 2020 Chromosome 6, # of SNPs: 283
Sat Oct 17 08:31:55 2020 Chromosome 7, # of SNPs: 245
Sat Oct 17 08:31:55 2020 Chromosome 8, # of SNPs: 234
Sat Oct 17 08:31:55 2020 Chromosome 9, # of SNPs: 202
Sat Oct 17 08:31:55 2020 Chromosome 10, # of SNPs: 224
Sat Oct 17 08:31:55 2020 Chromosome 11, # of SNPs: 223
Sat Oct 17 08:31:55 2020 Chromosome 12, # of SNPs: 208
Sat Oct 17 08:31:55 2020 Chromosome 13, # of SNPs: 172
Sat Oct 17 08:31:55 2020 Chromosome 14, # of SNPs: 147
Sat Oct 17 08:31:55 2020 Chromosome 15, # of SNPs: 121
Sat Oct 17 08:31:55 2020 Chromosome 16, # of SNPs: 129
Sat Oct 17 08:31:55 2020 Chromosome 17, # of SNPs: 116
Sat Oct 17 08:31:55 2020 Chromosome 18, # of SNPs: 129
Sat Oct 17 08:31:55 2020 Chromosome 19, # of SNPs: 73
Sat Oct 17 08:31:55 2020 Chromosome 20, # of SNPs: 106
Sat Oct 17 08:31:55 2020 Chromosome 21, # of SNPs: 62
Sat Oct 17 08:31:55 2020 Chromosome 22, # of SNPs: 51
Sat Oct 17 08:31:55 2020 Chromosome 23, # of SNPs: 204
Total # of SNPs selected:4570
FUNCTION: snpgdsBED2GDS
Start file conversion from PLINK BED to SNP GDS ...
BED file: "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/plinkhapmap.bed.gz"
SNP-major mode (Sample X SNP), 45.7K
FAM file: "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/plinkhapmap.fam.gz"
BIM file: "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/plinkhapmap.bim.gz"
Sat Oct 17 08:31:55 2020 (store sample id, snp id, position, and chromosome)
start writing: 60 samples, 5000 SNPs ...
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:31:55 2020 Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'HapMap.gds' (98.1K)
# of fragments: 38
save to 'HapMap.gds.tmp'
rename 'HapMap.gds.tmp' (97.8K, reduced: 240B)
# of fragments: 18
FUNCTION: snpgdsClose
FUNCTION: snpgdsCombineGeno
Create a GDS genotype file:
The new dataset consists of 10 samples and 3000 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Create a GDS genotype file:
The new dataset consists of 20 samples and 3000 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Merge SNP GDS files:
open 't1.gds' ...
10 samples, 3000 SNPs
open 't2.gds' ...
20 samples, 3000 SNPs
Concatenating samples (mapping to the first GDS file) ...
reference: 3000 SNPs (100.0%)
file 2: 0 allele flips, 0 ambiguous locus/loci
[no flip]: 3000
create 'test.gds': 30 samples, 3000 SNPs
FileFormat = SNP_ARRAY
writing genotypes ...
Clean up the fragments of GDS file:
open the file 'test.gds' (46.2K)
# of fragments: 32
save to 'test.gds.tmp'
rename 'test.gds.tmp' (46.0K, reduced: 204B)
# of fragments: 15
Done.
Create a GDS genotype file:
The new dataset consists of 279 samples and 100 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Create a GDS genotype file:
The new dataset consists of 279 samples and 200 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Merge SNP GDS files:
open 't1.gds' ...
279 samples, 100 SNPs
open 't2.gds' ...
279 samples, 200 SNPs
Concatenating SNPs ...
create 'test.gds': 279 samples, 300 SNPs
FileFormat = SNP_ARRAY
writing genotypes ...
Clean up the fragments of GDS file:
open the file 'test.gds' (19.1K)
# of fragments: 32
save to 'test.gds.tmp'
rename 'test.gds.tmp' (18.9K, reduced: 204B)
# of fragments: 15
Done.
FUNCTION: snpgdsCreateGeno
Principal Component Analysis (PCA) on genotypes:
Excluding 42 SNPs on non-autosomes
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 958
using 1 thread
# of principal components: 32
PCA: the sum of all selected genotypes (0,1,2) = 264760
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:31:55 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Sat Oct 17 08:31:56 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:31:56 2020 Done.
FUNCTION: snpgdsCreateGenoSet
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 76.12%, 545/716
Chromosome 2: 72.78%, 540/742
Chromosome 3: 74.71%, 455/609
Chromosome 4: 73.49%, 413/562
Chromosome 5: 76.86%, 435/566
Chromosome 6: 75.75%, 428/565
Chromosome 7: 75.42%, 356/472
Chromosome 8: 71.11%, 347/488
Chromosome 9: 77.88%, 324/416
Chromosome 10: 74.12%, 358/483
Chromosome 11: 77.85%, 348/447
Chromosome 12: 76.81%, 328/427
Chromosome 13: 76.16%, 262/344
Chromosome 14: 76.60%, 216/282
Chromosome 15: 76.34%, 200/262
Chromosome 16: 72.66%, 202/278
Chromosome 17: 73.91%, 153/207
Chromosome 18: 73.68%, 196/266
Chromosome 19: 85.00%, 102/120
Chromosome 20: 71.62%, 164/229
Chromosome 21: 76.98%, 97/126
Chromosome 22: 75.86%, 88/116
6,557 markers are selected in total.
Create a GDS genotype file:
The new dataset consists of 279 samples and 6557 SNPs
write sample.id
write snp.id
write snp.rs.id
write snp.position
write snp.chromosome
write snp.allele
SNP genotypes are stored in SNP-major mode (Sample X SNP).
FUNCTION: snpgdsCutTree
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Sat Oct 17 08:31:56 2020 0%
Dissimilarity: Sat Oct 17 08:31:58 2020 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
Create 4 groups.
FUNCTION: snpgdsDiss
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Sat Oct 17 08:31:59 2020 0%
Dissimilarity: Sat Oct 17 08:32:01 2020 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsDrawTree
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Sat Oct 17 08:32:01 2020 0%
Dissimilarity: Sat Oct 17 08:32:03 2020 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsEIGMIX
Eigen-analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Eigen-analysis: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:32:03 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Sat Oct 17 08:32:04 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:32:04 2020 Done.
FUNCTION: snpgdsErrMsg
FUNCTION: snpgdsExampleFileName
FUNCTION: snpgdsFst
Fst estimation on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
Method: Weir & Cockerham, 1984
# of Populations: 4
CEU (92), HCB (47), JPT (47), YRI (93)
Fst estimation on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
Method: Weir & Hill, 2002
# of Populations: 4
CEU (92), HCB (47), JPT (47), YRI (93)
FUNCTION: snpgdsGDS2BED
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: 0.95)
Converting from GDS to PLINK binary PED:
Working space: 279 samples, 8722 SNPs
Output a BIM file.
Output a BED file ...
Sat Oct 17 08:32:04 2020 0%
Sat Oct 17 08:32:04 2020 100%
Done.
FUNCTION: snpgdsGDS2Eigen
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: 0.95)
Converting from GDS to EIGENSOFT:
save to *.snp: 8722 snps
save to *.ind: 279 samples
Output: Sat Oct 17 08:32:04 2020 0%
Output: Sat Oct 17 08:32:05 2020 100%
Done.
FUNCTION: snpgdsGDS2PED
Converting from GDS to PLINK PED:
Output a MAP file DONE.
Output a PED file ...
Output: Sat Oct 17 08:32:05 2020 0%
Output: Sat Oct 17 08:32:05 2020 100%
FUNCTION: snpgdsGEN2GDS
running snpgdsGEN2GDS ...
FUNCTION: snpgdsGRM
Genetic Relationship Matrix (GRM, GCTA):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:32:05 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Sat Oct 17 08:32:06 2020 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:32:06 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:07 2020 Done.
FUNCTION: snpgdsGetGeno
Genotype matrix: 1000 SNPs X 279 samples
Genotype matrix: 279 samples X 1000 SNPs
FUNCTION: snpgdsHCluster
Individual dissimilarity analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Dissimilarity: the sum of all selected genotypes (0,1,2) = 2446510
Dissimilarity: Sat Oct 17 08:32:07 2020 0%
Dissimilarity: Sat Oct 17 08:32:08 2020 100%
Determine groups by permutation (Z threshold: 15, outlier threshold: 5):
Create 3 groups.
FUNCTION: snpgdsHWE
Keeping 716 SNPs according to chromosome 1
Excluding 160 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
FUNCTION: snpgdsIBDKING
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
No family is specified, and all individuals are treated as singletons.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:32:09 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:09 2020 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
No family is specified, and all individuals are treated as singletons.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:32:09 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Sat Oct 17 08:32:10 2020 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
# of families: 20, and within- and between-family relationship are estimated differently.
Relationship inference in the presence of population stratification.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:32:11 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:11 2020 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
Relationship inference in a homogeneous population.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
Sat Oct 17 08:32:11 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:11 2020 Done.
IBD analysis (KING method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
Relationship inference in a homogeneous population.
KING IBD: the sum of all selected genotypes (0,1,2) = 702139
Sat Oct 17 08:32:11 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:11 2020 Done.
FUNCTION: snpgdsIBDMLE
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,581 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
# of samples: 30
# of SNPs: 7,142
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 54.75%, 392/716
Chromosome 2: 54.31%, 403/742
Chromosome 3: 55.99%, 341/609
Chromosome 4: 56.58%, 318/562
Chromosome 5: 56.36%, 319/566
Chromosome 6: 52.74%, 298/565
Chromosome 7: 56.14%, 265/472
Chromosome 8: 51.84%, 253/488
Chromosome 9: 54.81%, 228/416
Chromosome 10: 49.90%, 241/483
Chromosome 11: 54.81%, 245/447
Chromosome 12: 54.57%, 233/427
Chromosome 13: 53.49%, 184/344
Chromosome 14: 56.03%, 158/282
Chromosome 15: 54.58%, 143/262
Chromosome 16: 54.68%, 152/278
Chromosome 17: 55.56%, 115/207
Chromosome 18: 55.64%, 148/266
Chromosome 19: 66.67%, 80/120
Chromosome 20: 53.28%, 122/229
Chromosome 21: 50.79%, 64/126
Chromosome 22: 51.72%, 60/116
4,762 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 30
# of SNPs: 250
using 1 thread
MLE IBD: the sum of all selected genotypes (0,1,2) = 7859
MLE IBD: Sat Oct 17 08:32:11 2020 0%
MLE IBD: Sat Oct 17 08:32:13 2020 100%
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.525, sd: 0.288
MLE IBD: the sum of all selected genotypes (0,1,2) = 6545
MLE IBD: Sat Oct 17 08:32:13 2020 0%
MLE IBD: Sat Oct 17 08:32:13 2020 100%
FUNCTION: snpgdsIBDMLELogLik
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,581 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
# of samples: 30
# of SNPs: 7,142
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 54.75%, 392/716
Chromosome 2: 54.31%, 403/742
Chromosome 3: 55.99%, 341/609
Chromosome 4: 56.58%, 318/562
Chromosome 5: 56.36%, 319/566
Chromosome 6: 52.74%, 298/565
Chromosome 7: 56.14%, 265/472
Chromosome 8: 51.84%, 253/488
Chromosome 9: 54.81%, 228/416
Chromosome 10: 49.90%, 241/483
Chromosome 11: 54.81%, 245/447
Chromosome 12: 54.57%, 233/427
Chromosome 13: 53.49%, 184/344
Chromosome 14: 56.03%, 158/282
Chromosome 15: 54.58%, 143/262
Chromosome 16: 54.68%, 152/278
Chromosome 17: 55.56%, 115/207
Chromosome 18: 55.64%, 148/266
Chromosome 19: 66.67%, 80/120
Chromosome 20: 53.28%, 122/229
Chromosome 21: 50.79%, 64/126
Chromosome 22: 51.72%, 60/116
4,762 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 30
# of SNPs: 250
using 1 thread
MLE IBD: the sum of all selected genotypes (0,1,2) = 7859
MLE IBD: Sat Oct 17 08:32:13 2020 0%
MLE IBD: Sat Oct 17 08:32:14 2020 100%
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.525, sd: 0.288
MLE IBD: the sum of all selected genotypes (0,1,2) = 6545
MLE IBD: Sat Oct 17 08:32:14 2020 0%
MLE IBD: Sat Oct 17 08:32:15 2020 100%
FUNCTION: snpgdsIBDMoM
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1,217 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 92
# of SNPs: 7,506
using 1 thread
PLINK IBD: the sum of all selected genotypes (0,1,2) = 702139
Sat Oct 17 08:32:15 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:15 2020 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 93
# of SNPs: 8,160
using 1 thread
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Sat Oct 17 08:32:15 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:15 2020 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 93
# of SNPs: 8,160
using 1 thread
Specifying allele frequencies, mean: 0.500, sd: 0.315
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Sat Oct 17 08:32:15 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:15 2020 Done.
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 8,160
using 1 thread
Specifying allele frequencies, mean: 0.500, sd: 0.315
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 203285
Sat Oct 17 08:32:15 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:15 2020 Done.
FUNCTION: snpgdsIBDSelection
IBD analysis (PLINK method of moment) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 563 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 93
# of SNPs: 8,160
using 1 thread
PLINK IBD: the sum of all selected genotypes (0,1,2) = 755648
Sat Oct 17 08:32:15 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:15 2020 Done.
FUNCTION: snpgdsIBS
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Sat Oct 17 08:32:15 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:15 2020 Done.
FUNCTION: snpgdsIBSNum
Identity-By-State (IBS) analysis on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
IBS: the sum of all selected genotypes (0,1,2) = 2446510
Sat Oct 17 08:32:16 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:16 2020 Done.
FUNCTION: snpgdsIndInb
Estimating individual inbreeding coefficients:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
FUNCTION: snpgdsIndInbCoef
FUNCTION: snpgdsIndivBeta
Individual Inbreeding and Relatedness (beta estimator):
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
Individual Beta: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:32:16 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:16 2020 Done.
FUNCTION: snpgdsLDMat
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 203
using 1 thread
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 56582
Linkage Disequilibrium (LD) estimation on genotypes:
# of samples: 279
# of SNPs: 203
using 1 thread
sliding window size: 203
method: composite
LD matrix: the sum of all selected genotypes (0,1,2) = 56582
FUNCTION: snpgdsLDpair
FUNCTION: snpgdsLDpruning
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 76.12%, 545/716
Chromosome 2: 72.78%, 540/742
Chromosome 3: 74.71%, 455/609
Chromosome 4: 73.49%, 413/562
Chromosome 5: 76.86%, 435/566
Chromosome 6: 75.75%, 428/565
Chromosome 7: 75.42%, 356/472
Chromosome 8: 71.11%, 347/488
Chromosome 9: 77.88%, 324/416
Chromosome 10: 74.12%, 358/483
Chromosome 11: 77.85%, 348/447
Chromosome 12: 76.81%, 328/427
Chromosome 13: 76.16%, 262/344
Chromosome 14: 76.60%, 216/282
Chromosome 15: 76.34%, 200/262
Chromosome 16: 72.66%, 202/278
Chromosome 17: 73.91%, 153/207
Chromosome 18: 73.68%, 196/266
Chromosome 19: 85.00%, 102/120
Chromosome 20: 71.62%, 164/229
Chromosome 21: 76.98%, 97/126
Chromosome 22: 75.86%, 88/116
6,557 markers are selected in total.
List of 22
$ chr1 : int [1:545] 1 2 4 5 7 10 12 14 15 16 ...
$ chr2 : int [1:540] 717 718 719 720 721 723 724 725 726 727 ...
$ chr3 : int [1:455] 1459 1460 1461 1464 1466 1468 1469 1471 1472 1473 ...
$ chr4 : int [1:413] 2068 2069 2070 2071 2072 2074 2075 2076 2077 2078 ...
$ chr5 : int [1:435] 2630 2631 2633 2635 2636 2637 2638 2640 2642 2643 ...
$ chr6 : int [1:428] 3196 3197 3198 3200 3201 3204 3205 3206 3207 3208 ...
$ chr7 : int [1:356] 3761 3762 3763 3766 3767 3768 3770 3771 3772 3773 ...
$ chr8 : int [1:347] 4233 4234 4235 4236 4237 4238 4239 4240 4241 4242 ...
$ chr9 : int [1:324] 4721 4722 4724 4727 4728 4730 4731 4732 4733 4735 ...
$ chr10: int [1:358] 5138 5139 5140 5143 5144 5145 5146 5147 5148 5149 ...
$ chr11: int [1:348] 5620 5621 5623 5624 5625 5626 5628 5629 5630 5631 ...
$ chr12: int [1:328] 6067 6068 6069 6070 6073 6074 6075 6077 6078 6079 ...
$ chr13: int [1:262] 6494 6497 6498 6499 6500 6501 6503 6505 6507 6509 ...
$ chr14: int [1:216] 6840 6841 6842 6843 6844 6845 6846 6847 6848 6850 ...
$ chr15: int [1:200] 7120 7121 7122 7124 7125 7126 7127 7128 7129 7130 ...
$ chr16: int [1:202] 7382 7383 7384 7385 7387 7388 7389 7391 7392 7394 ...
$ chr17: int [1:153] 7660 7661 7662 7663 7664 7665 7666 7667 7668 7669 ...
$ chr18: int [1:196] 7867 7868 7869 7870 7871 7872 7873 7874 7875 7877 ...
$ chr19: int [1:102] 8133 8135 8136 8137 8138 8139 8140 8141 8142 8144 ...
$ chr20: int [1:164] 8253 8254 8257 8258 8259 8260 8261 8262 8265 8266 ...
$ chr21: int [1:97] 8482 8484 8485 8486 8487 8488 8489 8490 8491 8492 ...
$ chr22: int [1:88] 8608 8609 8610 8612 8613 8614 8615 8617 8618 8619 ...
FUNCTION: snpgdsMergeGRM
Genetic Relationship Matrix (GRM, GCTA):
Excluding 2,288 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 6,800
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 1908966
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:32:17 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:17 2020 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,688 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 3,400
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 951558
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:32:18 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:18 2020 Done.
Genetic Relationship Matrix (GRM, GCTA):
Excluding 5,688 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 3,400
using 1 thread
GRM Calculation: the sum of all selected genotypes (0,1,2) = 957408
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:32:18 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 1s
Saving to the GDS file:
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:19 2020 Done.
GRM merging:
open 'tmp1.gds' (3,400 variants)
open 'tmp2.gds' (3,400 variants)
Weight: 0.5, 0.5
Output: tmp.gds
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
GRM merging:
open 'tmp1.gds' (3,400 variants)
open 'tmp2.gds' (3,400 variants)
Weight: 0.5, 0.5
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
FUNCTION: snpgdsOpen
FUNCTION: snpgdsOption
FUNCTION: snpgdsPCA
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
# of principal components: 32
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:32:20 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:20 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:32:20 2020 Done.
FUNCTION: snpgdsPCACorr
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
# of principal components: 32
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:32:21 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:21 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:32:21 2020 Done.
SNP Correlation:
# of samples: 279
# of SNPs: 9,088
using 1 thread
Correlation: the sum of all selected genotypes (0,1,2) = 2553065
Sat Oct 17 08:32:21 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:21 2020 Done.
SNP Correlation:
# of samples: 279
# of SNPs: 9,088
using 1 thread
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 2553065
Sat Oct 17 08:32:22 2020
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:22 2020 Done.
FUNCTION: snpgdsPCASNPLoading
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
# of principal components: 8
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:32:22 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:22 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:32:22 2020 Done.
SNP Loading:
# of samples: 279
# of SNPs: 8,722
using 1 thread
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 2446510
Sat Oct 17 08:32:22 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:22 2020 Done.
FUNCTION: snpgdsPCASampLoading
Principal Component Analysis (PCA) on genotypes:
Excluding 365 SNPs on non-autosomes
Excluding 1 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 8,722
using 1 thread
# of principal components: 8
PCA: the sum of all selected genotypes (0,1,2) = 2446510
CPU capabilities: Double-Precision SSE2
Sat Oct 17 08:32:23 2020 (internal increment: 11612)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:23 2020 Begin (eigenvalues and eigenvectors)
Sat Oct 17 08:32:23 2020 Done.
SNP Loading:
# of samples: 279
# of SNPs: 8,722
using 1 thread
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 2446510
Sat Oct 17 08:32:23 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:23 2020 Done.
Sample Loading:
# of samples: 100
# of SNPs: 8,722
using 1 thread
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 878146
Sat Oct 17 08:32:23 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:23 2020 Done.
FUNCTION: snpgdsPED2GDS
Converting from GDS to PLINK PED:
Output a MAP file DONE.
Output a PED file ...
Output: Sat Oct 17 08:32:23 2020 0%
Output: Sat Oct 17 08:32:24 2020 100%
PLINK PED/MAP to GDS Format:
Import 9088 variants from 'tmp.map'
Chromosome:
1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7
716 483 447 427 344 282 262 278 207 266 120 742 229 126 116 609 562 566 565 472
8 9 X
488 416 365
Reading 'tmp.ped'
Output: 'test.gds'
Import 279 samples
Transpose the genotypic matrix ...
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test.gds' (1.3M)
# of fragments: 50
save to 'test.gds.tmp'
rename 'test.gds.tmp' (711.4K, reduced: 618.7K)
# of fragments: 26
FUNCTION: snpgdsPairIBD
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,646 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
# of samples: 93
# of SNPs: 7,077
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 62.29%, 446/716
Chromosome 2: 62.67%, 465/742
Chromosome 3: 59.93%, 365/609
Chromosome 4: 64.23%, 361/562
Chromosome 5: 62.37%, 353/566
Chromosome 6: 59.82%, 338/565
Chromosome 7: 63.14%, 298/472
Chromosome 8: 57.58%, 281/488
Chromosome 9: 62.98%, 262/416
Chromosome 10: 60.46%, 292/483
Chromosome 11: 63.09%, 282/447
Chromosome 12: 62.76%, 268/427
Chromosome 13: 63.08%, 217/344
Chromosome 14: 63.83%, 180/282
Chromosome 15: 63.74%, 167/262
Chromosome 16: 62.23%, 173/278
Chromosome 17: 65.70%, 136/207
Chromosome 18: 59.40%, 158/266
Chromosome 19: 68.33%, 82/120
Chromosome 20: 66.38%, 152/229
Chromosome 21: 61.11%, 77/126
Chromosome 22: 57.76%, 67/116
5,420 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
MLE IBD: the sum of all selected genotypes (0,1,2) = 6112
MLE IBD: Sat Oct 17 08:32:25 2020 0%
MLE IBD: Sat Oct 17 08:32:26 2020 100%
IBD analysis (PLINK method of moment) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 6112
Sat Oct 17 08:32:26 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:26 2020 Done.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
MLE IBD: the sum of all selected genotypes (0,1,2) = 6112
MLE IBD: Sat Oct 17 08:32:26 2020 0%
MLE IBD: Sat Oct 17 08:32:26 2020 100%
Genotype matrix: 250 SNPs X 25 samples
[1] -370.7482
[1] -402.2141
[1] -383.7897
[1] -377.9084
[1] -381.3139
[1] -397.5581
[1] -378.3344
[1] -370.703
[1] -376.103
[1] -377.7911
[1] -375.5425
[1] -373.13
[1] -383.6992
[1] -393.5194
[1] -371.9843
[1] -369.6468
[1] -374.5139
[1] -377.841
[1] -387.5622
[1] -377.1646
[1] -377.4659
[1] -375.2204
[1] -372.0639
[1] -379.816
FUNCTION: snpgdsPairIBDMLELogLik
SNP pruning based on LD:
Excluding 365 SNPs on non-autosomes
Excluding 1,646 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.05)
# of samples: 93
# of SNPs: 7,077
using 1 thread
sliding window: 500,000 basepairs, Inf SNPs
|LD| threshold: 0.2
method: composite
Chromosome 1: 62.29%, 446/716
Chromosome 2: 62.67%, 465/742
Chromosome 3: 59.93%, 365/609
Chromosome 4: 64.23%, 361/562
Chromosome 5: 62.37%, 353/566
Chromosome 6: 59.82%, 338/565
Chromosome 7: 63.14%, 298/472
Chromosome 8: 57.58%, 281/488
Chromosome 9: 62.98%, 262/416
Chromosome 10: 60.46%, 292/483
Chromosome 11: 63.09%, 282/447
Chromosome 12: 62.76%, 268/427
Chromosome 13: 63.08%, 217/344
Chromosome 14: 63.83%, 180/282
Chromosome 15: 63.74%, 167/262
Chromosome 16: 62.23%, 173/278
Chromosome 17: 65.70%, 136/207
Chromosome 18: 59.40%, 158/266
Chromosome 19: 68.33%, 82/120
Chromosome 20: 66.38%, 152/229
Chromosome 21: 61.11%, 77/126
Chromosome 22: 57.76%, 67/116
5,420 markers are selected in total.
Identity-By-Descent analysis (MLE) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
MLE IBD: the sum of all selected genotypes (0,1,2) = 6112
MLE IBD: Sat Oct 17 08:32:27 2020 0%
MLE IBD: Sat Oct 17 08:32:28 2020 100%
IBD analysis (PLINK method of moment) on genotypes:
Excluding 8,838 SNPs (non-autosomes or non-selection)
Excluding 0 SNP (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 25
# of SNPs: 250
using 1 thread
Specifying allele frequencies, mean: 0.486, sd: 0.284
*** A correction factor based on allele count is not used, since the allele frequencies are specified.
PLINK IBD: the sum of all selected genotypes (0,1,2) = 6112
Sat Oct 17 08:32:28 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:28 2020 Done.
Genotype matrix: 250 SNPs X 25 samples
[1] -370.7482
[1] -402.2141
[1] -383.7897
[1] -377.9084
[1] -381.3139
[1] -397.5581
[1] -378.3344
[1] -370.703
[1] -376.103
[1] -377.7911
[1] -375.5425
[1] -373.13
[1] -383.6992
[1] -393.5194
[1] -371.9843
[1] -369.6468
[1] -374.5139
[1] -377.841
[1] -387.5622
[1] -377.1646
[1] -377.4659
[1] -375.2204
[1] -372.0639
[1] -379.816
FUNCTION: snpgdsPairScore
Excluding 365 SNPs on non-autosomes
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
List of 3
$ sample.id: chr [1:120] "NA19139" "NA19160" "NA07034" "NA12814" ...
$ snp.id : int [1:8723] 1 2 3 4 5 6 7 8 9 10 ...
$ score :'data.frame': 60 obs. of 5 variables:
..$ Avg : num [1:60] 1.72 1.73 1.71 1.72 1.73 ...
..$ SD : num [1:60] 0.452 0.443 0.457 0.45 0.443 ...
..$ Num : int [1:60] 8684 8627 8669 8637 8682 8634 8654 8678 8680 8679 ...
..$ Sample1: chr [1:60] "NA19139" "NA10847" "NA18515" "NA19129" ...
..$ Sample2: chr [1:60] "NA19138" "NA12146" "NA18516" "NA19128" ...
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
List of 3
$ sample.id: chr [1:120] "NA19139" "NA19160" "NA07034" "NA12814" ...
$ snp.id : int [1:8723] 1 2 3 4 5 6 7 8 9 10 ...
$ score :'data.frame': 60 obs. of 5 variables:
..$ Avg : num [1:60] 0.999 1 1 1 1 ...
..$ SD : num [1:60] 0.024 0 0.0186 0.0215 0.0215 ...
..$ Num : int [1:60] 8684 8627 8669 8637 8682 8634 8654 8678 8680 8679 ...
..$ Sample1: chr [1:60] "NA19139" "NA10847" "NA18515" "NA19129" ...
..$ Sample2: chr [1:60] "NA19138" "NA12146" "NA18516" "NA19128" ...
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
List of 3
$ sample.id: chr [1:120] "NA19139" "NA19160" "NA07034" "NA12814" ...
$ snp.id : int [1:8723] 1 2 3 4 5 6 7 8 9 10 ...
$ score : num [1:3, 1:8723] 1.75 0.437 60 1.583 0.497 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:3] "Avg" "SD" "Num"
.. ..$ : NULL
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
List of 3
$ sample.id: chr [1:120] "NA19139" "NA19160" "NA07034" "NA12814" ...
$ snp.id : int [1:8723] 1 2 3 4 5 6 7 8 9 10 ...
$ score : int [1:60, 1:8723] 1 1 2 2 2 2 2 1 2 2 ...
Pair Score Calculation:
# of samples: 120
# of SNPs: 8,723
Method: IBS
Output: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_x64\tmp.gds
Genotype Score: the sum of all selected genotypes (0,1,2) = 1050236
FUNCTION: snpgdsSNPList
FUNCTION: snpgdsSNPListClass
FUNCTION: snpgdsSNPListIntersect
FUNCTION: snpgdsSNPRateFreq
FUNCTION: snpgdsSampMissRate
FUNCTION: snpgdsSelectSNP
Excluding 365 SNPs on non-autosomes
Excluding 1,221 SNPs (monomorphic: TRUE, MAF: 0.05, missing rate: 0.95)
FUNCTION: snpgdsSlidingWindow
Sliding Window Analysis:
Excluding 8 SNPs (monomorphic: TRUE, MAF: NaN, missing rate: NaN)
# of samples: 279
# of SNPs: 9,080
using 1 thread
window size: 500000, shift: 100000 (basepair)
Chromosome Set: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23
Sat Oct 17 08:32:29 2020, Chromosome 1 (716 SNPs), 2448 windows
Sat Oct 17 08:32:29 2020, Chromosome 2 (742 SNPs), 2416 windows
Sat Oct 17 08:32:29 2020, Chromosome 3 (609 SNPs), 1985 windows
Sat Oct 17 08:32:29 2020, Chromosome 4 (562 SNPs), 1894 windows
Sat Oct 17 08:32:29 2020, Chromosome 5 (566 SNPs), 1797 windows
Sat Oct 17 08:32:29 2020, Chromosome 6 (565 SNPs), 1694 windows
Sat Oct 17 08:32:29 2020, Chromosome 7 (472 SNPs), 1573 windows
Sat Oct 17 08:32:29 2020, Chromosome 8 (488 SNPs), 1445 windows
Sat Oct 17 08:32:29 2020, Chromosome 9 (416 SNPs), 1393 windows
Sat Oct 17 08:32:29 2020, Chromosome 10 (483 SNPs), 1343 windows
Sat Oct 17 08:32:29 2020, Chromosome 11 (447 SNPs), 1338 windows
Sat Oct 17 08:32:29 2020, Chromosome 12 (427 SNPs), 1316 windows
Sat Oct 17 08:32:29 2020, Chromosome 13 (344 SNPs), 948 windows
Sat Oct 17 08:32:29 2020, Chromosome 14 (281 SNPs), 847 windows
Sat Oct 17 08:32:29 2020, Chromosome 15 (262 SNPs), 774 windows
Sat Oct 17 08:32:29 2020, Chromosome 16 (278 SNPs), 873 windows
Sat Oct 17 08:32:30 2020, Chromosome 17 (207 SNPs), 773 windows
Sat Oct 17 08:32:30 2020, Chromosome 18 (266 SNPs), 753 windows
Sat Oct 17 08:32:30 2020, Chromosome 19 (120 SNPs), 627 windows
Sat Oct 17 08:32:30 2020, Chromosome 20 (229 SNPs), 602 windows
Sat Oct 17 08:32:30 2020, Chromosome 21 (126 SNPs), 311 windows
Sat Oct 17 08:32:30 2020, Chromosome 22 (116 SNPs), 312 windows
Sat Oct 17 08:32:30 2020, Chromosome 23 (358 SNPs), 1507 windows
Sat Oct 17 08:32:30 2020 Done.
FUNCTION: snpgdsSummary
The file name: C:\Users\biocbuild\bbs-3.11-bioc\R\library\SNPRelate\extdata\hapmap_geno.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in SNP-major mode (Sample X SNP).
FUNCTION: snpgdsTranspose
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_x64\test.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in SNP-major mode (Sample X SNP).
SNP genotypes: 279 samples, 9088 SNPs
Genotype matrix is being transposed ...
Clean up the fragments of GDS file:
open the file 'test.gds' (1.3M)
# of fragments: 28
save to 'test.gds.tmp'
rename 'test.gds.tmp' (709.6K, reduced: 619.1K)
# of fragments: 26
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_x64\test.gds
The total number of samples: 279
The total number of SNPs: 9088
SNP genotypes are stored in individual-major mode (SNP X Sample).
FUNCTION: snpgdsVCF2GDS
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
Start file conversion from VCF to SNP GDS ...
Method: exacting biallelic SNPs
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 2 variants.
+ genotype { Bit2 3x2, 2B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test1.gds' (2.9K)
# of fragments: 46
save to 'test1.gds.tmp'
rename 'test1.gds.tmp' (2.6K, reduced: 312B)
# of fragments: 20
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_x64\test1.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start file conversion from VCF to SNP GDS ...
Method: exacting biallelic SNPs
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 2 variants.
+ genotype { Bit2 3x2, 2B } *
SNP genotypes: 3 samples, 2 SNPs
Genotype matrix is being transposed ...
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test2.gds' (3.0K)
# of fragments: 48
save to 'test2.gds.tmp'
rename 'test2.gds.tmp' (2.6K, reduced: 417B)
# of fragments: 20
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_x64\test2.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in individual-major mode (SNP X Sample).
Start file conversion from VCF to SNP GDS ...
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
SNP genotypes: 3 samples, 5 SNPs
Genotype matrix is being transposed ...
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test3.gds' (3.1K)
# of fragments: 48
save to 'test3.gds.tmp'
rename 'test3.gds.tmp' (2.7K, reduced: 419B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_x64\test3.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in individual-major mode (SNP X Sample).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
Start file conversion from VCF to SNP GDS ...
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test4.gds' (3.0K)
# of fragments: 46
save to 'test4.gds.tmp'
rename 'test4.gds.tmp' (2.7K, reduced: 312B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_x64\test4.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
Start file conversion from VCF to SNP GDS ...
Method: dosage (0,1,2) of reference allele for all variant sites
Number of samples: 3
Parsing "C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf" ...
import 5 variants.
+ genotype { Bit2 3x5, 4B } *
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file 'test5.gds' (3.0K)
# of fragments: 46
save to 'test5.gds.tmp'
rename 'test5.gds.tmp' (2.7K, reduced: 312B)
# of fragments: 20
Some of 'snp.allele' are not standard (e.g., T/A,G).
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_x64\test5.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
FUNCTION: snpgdsVCF2GDS_R
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
20 14370 rs6054257 G A 29 PASS NS=3;DP=14;AF=0.5;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
20 17330 . T A 3 q10 NS=3;DP=11;AF=0.017 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3
20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4
20 1230237 . T . 47 PASS NS=3;DP=13;AA=T GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
20 1234567 microsat1 GTC G,GTCT 50 PASS NS=3;DP=9;AA=G GT:GQ:DP 0/1:35:4 0/2:17:2 1/1:40:3
Start snpgdsVCF2GDS ...
Extracting bi-allelic and polymorhpic SNPs.
Scanning ...
file: C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Sat Oct 17 08:32:30 2020 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 2 SNPs ...
file: C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf
[1] 1
Sat Oct 17 08:32:30 2020 Done.
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_x64\test1.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start snpgdsVCF2GDS ...
Extracting bi-allelic and polymorhpic SNPs.
Scanning ...
file: C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Sat Oct 17 08:32:30 2020 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 2 SNPs ...
file: C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf
[1] 1
Sat Oct 17 08:32:30 2020 Done.
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_x64\test2.gds
The total number of samples: 3
The total number of SNPs: 2
SNP genotypes are stored in SNP-major mode (Sample X SNP).
Start snpgdsVCF2GDS ...
Storing dosage of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants.
Scanning ...
file: C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Sat Oct 17 08:32:31 2020 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 5 SNPs ...
file: C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf
Sat Oct 17 08:32:31 2020 Done.
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_x64\test3.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
Start snpgdsVCF2GDS ...
Storing dosage of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants.
Scanning ...
file: C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf
content: 5 rows x 12 columns
Sat Oct 17 08:32:31 2020 store sample id, snp id, position, and chromosome.
start writing: 3 samples, 5 SNPs ...
file: C:/Users/biocbuild/bbs-3.11-bioc/R/library/SNPRelate/extdata/sequence.vcf
Sat Oct 17 08:32:31 2020 Done.
Some of 'snp.allele' are not standard (e.g., A/G,T).
The file name: C:\Users\biocbuild\bbs-3.11-bioc\meat\SNPRelate.Rcheck\tests_x64\test4.gds
The total number of samples: 3
The total number of SNPs: 5
SNP genotypes are stored in SNP-major mode (Sample X SNP).
The number of valid samples: 3
The number of biallelic unique SNPs: 2
SNP Correlation:
# of samples: 90
# of SNPs: 9,088
using 1 thread
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Sat Oct 17 08:32:32 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:32 2020 Done.
SNP Correlation:
# of samples: 90
# of SNPs: 9,088
using 1 thread
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Sat Oct 17 08:32:32 2020
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:32 2020 Done.
SNP Loading:
# of samples: 90
# of SNPs: 8,695
using 1 thread
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 787449
Sat Oct 17 08:32:32 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:32 2020 Done.
Sample Loading:
# of samples: 100
# of SNPs: 8,695
using 1 thread
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 875255
Sat Oct 17 08:32:32 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:32 2020 Done.
SNP Correlation:
# of samples: 90
# of SNPs: 9,088
using 2 threads
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Sat Oct 17 08:32:33 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:33 2020 Done.
SNP Correlation:
# of samples: 90
# of SNPs: 9,088
using 2 threads
Creating 'test.gds' ...
Correlation: the sum of all selected genotypes (0,1,2) = 824424
Sat Oct 17 08:32:33 2020
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:33 2020 Done.
SNP Loading:
# of samples: 90
# of SNPs: 8,695
using 1 thread
using the top 8 eigenvectors
SNP Loading: the sum of all selected genotypes (0,1,2) = 787449
Sat Oct 17 08:32:33 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:33 2020 Done.
Sample Loading:
# of samples: 100
# of SNPs: 8,695
using 1 thread
using the top 8 eigenvectors
Sample Loading: the sum of all selected genotypes (0,1,2) = 875255
Sat Oct 17 08:32:33 2020 (internal increment: 65536)
[..................................................] 0%, ETC: ---
[==================================================] 100%, completed, 0s
Sat Oct 17 08:32:33 2020 Done.
RUNIT TEST PROTOCOL -- Sat Oct 17 08:32:33 2020
***********************************************
Number of test functions: 13
Number of errors: 0
Number of failures: 0
1 Test Suite :
SNPRelate RUnit Tests - 13 test functions, 0 errors, 0 failures
Number of test functions: 13
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
51.87 2.40 54.45
|
