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

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.

AuthorXiuwen Zheng [aut, cre, cph], Stephanie Gogarten [ctb], Cathy Laurie [ctb], Bruce Weir [ctb, ths]
Date of publicationNone
MaintainerXiuwen Zheng <zhengx@u.washington.edu>
LicenseGPL-3
Version1.8.0
http://github.com/zhengxwen/SNPRelate, http://corearray.sourceforge.net/tutorials/SNPRelate/

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

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