SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

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Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed an R package SNPRelate to provide a binary format for single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS format offers the efficient operations specifically designed for integers with two bits, since a SNP could occupy only two bits. SNPRelate is also designed to accelerate two key computations on SNP data using parallel computing for multi-core symmetric multiprocessing computer architectures: Principal Component Analysis (PCA) and relatedness analysis using Identity-By-Descent measures. The SNP GDS format is also used by the GWASTools package with the support of S4 classes and generic functions. The extended GDS format is implemented in the SeqArray package to support the storage of single nucleotide variations (SNVs), insertion/deletion polymorphism (indel) and structural variation calls.

Author
Xiuwen Zheng [aut, cre, cph], Stephanie Gogarten [ctb], Cathy Laurie [ctb], Bruce Weir [ctb, ths]
Date of publication
None
Maintainer
Xiuwen Zheng <zhengx@u.washington.edu>
License
GPL-3
Version
1.8.0
URLs

View on Bioconductor

Man pages

hapmap_geno
SNP genotypes of HapMap samples
snpgdsAdmixProp
Estimate ancestral proportions from the eigen-analysis
snpgdsAlleleSwitch
Allele-switching
snpgdsApartSelection
Select SNPs with a basepair distance
snpgdsBED2GDS
Conversion from PLINK BED to GDS
snpgdsClose
Close the SNP GDS File
snpgdsCombineGeno
Merge SNP datasets
snpgdsCreateGeno
Create a SNP genotype dataset from a matrix
snpgdsCreateGenoSet
Create a SNP genotype dataset from a GDS file
snpgdsCutTree
Determine clusters of individuals
snpgdsDiss
Individual dissimilarity analysis
snpgdsDrawTree
Draw a dendrogram
snpgdsEIGMIX
Eigen-analysis on SNP genotype data
snpgdsErrMsg
Get the last error information
snpgdsExampleFileName
Example GDS file
SNPGDSFileClass-class
SNPGDSFileClass
snpgdsFst
F-statistics (fixation indices)
snpgdsGDS2BED
Conversion from GDS to PLINK BED
snpgdsGDS2Eigen
Conversion from GDS to Eigen (EIGENSTRAT)
snpgdsGDS2PED
Conversion from GDS to PED
snpgdsGEN2GDS
Conversion from Oxford GEN format to GDS
snpgdsGetGeno
To get a genotype matrix
snpgdsGRM
Genetic Relationship Matrix (GRM) for SNP genotype data
snpgdsHCluster
Hierarchical cluster analysis
snpgdsHWE
Statistical test of Hardy-Weinberg Equilibrium
snpgdsIBDKING
KING method of moment for the identity-by-descent (IBD)...
snpgdsIBDMLE
Maximum likelihood estimation (MLE) for the...
snpgdsIBDMLELogLik
Log likelihood for MLE method in the Identity-By-Descent...
snpgdsIBDMoM
PLINK method of moment (MoM) for the Identity-By-Descent...
snpgdsIBDSelection
Get a table of IBD coefficients
snpgdsIBS
Identity-By-State (IBS) proportion
snpgdsIBSNum
Identity-By-State (IBS)
snpgdsIndInb
Individual Inbreeding Coefficients
snpgdsIndInbCoef
Individual Inbreeding Coefficient
snpgdsIndivBeta
Individual inbreeding and relatedness estimation (beta...
snpgdsLDMat
Linkage Disequilibrium (LD) analysis
snpgdsLDpair
Linkage Disequilibrium (LD)
snpgdsLDpruning
Linkage Disequilibrium (LD) based SNP pruning
snpgdsOpen
Open a SNP GDS File
snpgdsOption
Option settings: chromosome coding, etc
snpgdsPairIBD
Calculate Identity-By-Descent (IBD) Coefficients
snpgdsPairIBDMLELogLik
Log likelihood for MLE method in the Identity-By-Descent...
snpgdsPairScore
Genotype Score for Pairs of Individuals
snpgdsPCA
Principal Component Analysis (PCA) on SNP genotype data
snpgdsPCACorr
PC-correlated SNPs in principal component analysis
snpgdsPCASampLoading
Project individuals onto existing principal component axes
snpgdsPCASNPLoading
SNP loadings in principal component analysis
snpgdsPED2GDS
Conversion from PLINK PED to GDS
snpgdsSampMissRate
Missing Rate of Samples
snpgdsSelectSNP
SNP selection
snpgdsSlidingWindow
Sliding window
snpgdsSNPList
Create a SNP list object
snpgdsSNPListClass
the class of a SNP list
snpgdsSNPListIntersect
Get a common SNP list between two SNP list objects
snpgdsSNPListStrand
Switch allele strand.
snpgdsSNPRateFreq
Allele Frequency, Minor Allele Frequency, Missing Rate of...
snpgdsSummary
Summary of GDS genotype file
snpgdsTranspose
Transpose genotypic matrix
snpgdsVCF2GDS
Reformat VCF file(s)
snpgdsVCF2GDS_R
Reformat a VCF file (R implementation)
SNPRelate-package
Parallel Computing Toolset for Genome-Wide Association...

Files in this package

SNPRelate/DESCRIPTION
SNPRelate/NAMESPACE
SNPRelate/NEWS
SNPRelate/R
SNPRelate/R/AllUtilities.R
SNPRelate/R/Conversion.R
SNPRelate/R/Conversion2.R
SNPRelate/R/IBD.R
SNPRelate/R/IBS.R
SNPRelate/R/Internal.R
SNPRelate/R/LD.R
SNPRelate/R/PCA.R
SNPRelate/README.md
SNPRelate/build
SNPRelate/build/vignette.rds
SNPRelate/data
SNPRelate/data/hapmap_geno.RData
SNPRelate/inst
SNPRelate/inst/CITATION
SNPRelate/inst/doc
SNPRelate/inst/doc/SNPRelateTutorial.R
SNPRelate/inst/doc/SNPRelateTutorial.Rmd
SNPRelate/inst/doc/SNPRelateTutorial.html
SNPRelate/inst/extdata
SNPRelate/inst/extdata/hapmap_geno.gds
SNPRelate/inst/extdata/plinkhapmap.bed.gz
SNPRelate/inst/extdata/plinkhapmap.bim.gz
SNPRelate/inst/extdata/plinkhapmap.fam.gz
SNPRelate/inst/extdata/sequence.vcf
SNPRelate/inst/unitTests
SNPRelate/inst/unitTests/test_Func.R
SNPRelate/inst/unitTests/test_IBS.R
SNPRelate/inst/unitTests/test_KING.R
SNPRelate/inst/unitTests/test_LD.R
SNPRelate/inst/unitTests/test_PCA.R
SNPRelate/inst/unitTests/test_PLINK.R
SNPRelate/inst/unitTests/test_Transpose.R
SNPRelate/inst/unitTests/test_examples.R
SNPRelate/inst/unitTests/valid
SNPRelate/inst/unitTests/valid/Validate.IBS.RData
SNPRelate/inst/unitTests/valid/Validate.KING.RData
SNPRelate/inst/unitTests/valid/Validate.MoM.RData
SNPRelate/inst/unitTests/valid/Validate.PCA.RData
SNPRelate/man
SNPRelate/man/SNPGDSFileClass-class.Rd
SNPRelate/man/SNPRelate-package.Rd
SNPRelate/man/hapmap_geno.Rd
SNPRelate/man/snpgdsAdmixProp.Rd
SNPRelate/man/snpgdsAlleleSwitch.Rd
SNPRelate/man/snpgdsApartSelection.Rd
SNPRelate/man/snpgdsBED2GDS.Rd
SNPRelate/man/snpgdsClose.Rd
SNPRelate/man/snpgdsCombineGeno.Rd
SNPRelate/man/snpgdsCreateGeno.Rd
SNPRelate/man/snpgdsCreateGenoSet.Rd
SNPRelate/man/snpgdsCutTree.Rd
SNPRelate/man/snpgdsDiss.Rd
SNPRelate/man/snpgdsDrawTree.Rd
SNPRelate/man/snpgdsEIGMIX.Rd
SNPRelate/man/snpgdsErrMsg.Rd
SNPRelate/man/snpgdsExampleFileName.Rd
SNPRelate/man/snpgdsFst.Rd
SNPRelate/man/snpgdsGDS2BED.Rd
SNPRelate/man/snpgdsGDS2Eigen.Rd
SNPRelate/man/snpgdsGDS2PED.Rd
SNPRelate/man/snpgdsGEN2GDS.Rd
SNPRelate/man/snpgdsGRM.Rd
SNPRelate/man/snpgdsGetGeno.Rd
SNPRelate/man/snpgdsHCluster.Rd
SNPRelate/man/snpgdsHWE.Rd
SNPRelate/man/snpgdsIBDKING.Rd
SNPRelate/man/snpgdsIBDMLE.Rd
SNPRelate/man/snpgdsIBDMLELogLik.Rd
SNPRelate/man/snpgdsIBDMoM.Rd
SNPRelate/man/snpgdsIBDSelection.Rd
SNPRelate/man/snpgdsIBS.Rd
SNPRelate/man/snpgdsIBSNum.Rd
SNPRelate/man/snpgdsIndInb.Rd
SNPRelate/man/snpgdsIndInbCoef.Rd
SNPRelate/man/snpgdsIndivBeta.Rd
SNPRelate/man/snpgdsLDMat.Rd
SNPRelate/man/snpgdsLDpair.Rd
SNPRelate/man/snpgdsLDpruning.Rd
SNPRelate/man/snpgdsOpen.Rd
SNPRelate/man/snpgdsOption.Rd
SNPRelate/man/snpgdsPCA.Rd
SNPRelate/man/snpgdsPCACorr.Rd
SNPRelate/man/snpgdsPCASNPLoading.Rd
SNPRelate/man/snpgdsPCASampLoading.Rd
SNPRelate/man/snpgdsPED2GDS.Rd
SNPRelate/man/snpgdsPairIBD.Rd
SNPRelate/man/snpgdsPairIBDMLELogLik.Rd
SNPRelate/man/snpgdsPairScore.Rd
SNPRelate/man/snpgdsSNPList.Rd
SNPRelate/man/snpgdsSNPListClass.Rd
SNPRelate/man/snpgdsSNPListIntersect.Rd
SNPRelate/man/snpgdsSNPListStrand.Rd
SNPRelate/man/snpgdsSNPRateFreq.Rd
SNPRelate/man/snpgdsSampMissRate.Rd
SNPRelate/man/snpgdsSelectSNP.Rd
SNPRelate/man/snpgdsSlidingWindow.Rd
SNPRelate/man/snpgdsSummary.Rd
SNPRelate/man/snpgdsTranspose.Rd
SNPRelate/man/snpgdsVCF2GDS.Rd
SNPRelate/man/snpgdsVCF2GDS_R.Rd
SNPRelate/src
SNPRelate/src/ConvToGDS.cpp
SNPRelate/src/Makevars
SNPRelate/src/Makevars.win
SNPRelate/src/R_SNPRelate.c
SNPRelate/src/SNPRelate.cpp
SNPRelate/src/ThreadPool.cpp
SNPRelate/src/ThreadPool.h
SNPRelate/src/dGenGWAS.cpp
SNPRelate/src/dGenGWAS.h
SNPRelate/src/dVect.cpp
SNPRelate/src/dVect.h
SNPRelate/src/genBeta.cpp
SNPRelate/src/genFst.cpp
SNPRelate/src/genHWE.cpp
SNPRelate/src/genIBD.cpp
SNPRelate/src/genIBS.cpp
SNPRelate/src/genKING.cpp
SNPRelate/src/genLD.cpp
SNPRelate/src/genPCA.cpp
SNPRelate/src/genRec.cpp
SNPRelate/src/genSlideWin.cpp
SNPRelate/tests
SNPRelate/tests/runTests.R
SNPRelate/vignettes
SNPRelate/vignettes/SNPRelate-Flowchart.png
SNPRelate/vignettes/SNPRelateTutorial.Rmd
SNPRelate/vignettes/link.png