SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
Version 1.10.1

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]
Bioconductor views Genetics Infrastructure PrincipalComponent StatisticalMethod
Date of publicationNone
MaintainerXiuwen Zheng <zhengx@u.washington.edu>
LicenseGPL-3
Version1.10.1
URL http://github.com/zhengxwen/SNPRelate http://corearray.sourceforge.net/tutorials/SNPRelate/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SNPRelate")

Getting started

Package overview
README.md
Tutorials for the R/Bioconductor Package SNPRelate

Popular man pages

snpgdsDrawTree: Draw a dendrogram
snpgdsFst: F-statistics (fixation indices)
snpgdsGRM: Genetic Relationship Matrix (GRM) for SNP genotype data
snpgdsIBS: Identity-By-State (IBS) proportion
snpgdsIndivBeta: Individual inbreeding and relatedness estimation (beta...
snpgdsPCA: Principal Component Analysis (PCA) on SNP genotype data
snpgdsPED2GDS: Conversion from PLINK PED to GDS
See all...

All man pages Function index File listing

Man pages

hapmap_geno: SNP genotypes of HapMap samples
snpgdsAdmixPlot: Plot Ancestry Proportions
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...

Functions

CheckFile Source code
CloseConnection Source code
InitFile Source code
InitFile2 Source code
OpenConnBin Source code
OpenConnText Source code
SNPGDSFileClass Man page
SNPGDSFileClass-class Man page
SNPRelate Man page
SNPRelate-package Man page
astStr Source code
hapmap_geno Man page
onAttach Source code
paramFst Source code
plot.snpgdsEigMixClass Man page Source code
plot.snpgdsPCAClass Man page Source code
plural Source code
pretty Source code
seldim Source code
snpgdsAdmixPlot Man page Source code
snpgdsAdmixProp Man page Source code
snpgdsAdmixTable Man page Source code
snpgdsAlleleSwitch Man page Source code
snpgdsApartSelection Man page Source code
snpgdsBED2GDS Man page Source code
snpgdsClose Man page Source code
snpgdsCombineGeno Man page Source code
snpgdsCreateGeno Man page Source code
snpgdsCreateGenoSet Man page Source code
snpgdsCutTree Man page Source code
snpgdsDiss Man page Source code
snpgdsDrawTree Man page Source code
snpgdsEIGMIX Man page Source code
snpgdsErrMsg Man page Source code
snpgdsExampleFileName Man page Source code
snpgdsFst Man page Source code
snpgdsGDS2BED Man page Source code
snpgdsGDS2Eigen Man page Source code
snpgdsGDS2PED Man page Source code
snpgdsGEN2GDS Man page Source code
snpgdsGRM Man page Source code
snpgdsGetGeno Man page Source code
snpgdsHCluster Man page Source code
snpgdsHWE Man page Source code
snpgdsIBDKING Man page Source code
snpgdsIBDMLE Man page Source code
snpgdsIBDMLELogLik Man page Source code
snpgdsIBDMoM Man page Source code
snpgdsIBDSelection Man page Source code
snpgdsIBS Man page Source code
snpgdsIBSNum Man page Source code
snpgdsImport Source code
snpgdsIndInb Man page Source code
snpgdsIndInbCoef Man page Source code
snpgdsIndivBeta Man page Source code
snpgdsLDMat Man page Source code
snpgdsLDpair Man page Source code
snpgdsLDpruning Man page Source code
snpgdsOpen Man page Source code
snpgdsOption Man page Source code
snpgdsPCA Man page Source code
snpgdsPCACorr Man page Source code
snpgdsPCASNPLoading Man page Source code
snpgdsPCASampLoading Man page Source code
snpgdsPED2GDS Man page Source code
snpgdsPairIBD Man page Source code
snpgdsPairIBDMLELogLik Man page Source code
snpgdsPairScore Man page Source code
snpgdsSNPList Man page Source code
snpgdsSNPListClass Man page
snpgdsSNPListIntersect Man page Source code
snpgdsSNPListStrand Man page Source code
snpgdsSNPRateFreq Man page Source code
snpgdsSampMissRate Man page Source code
snpgdsSelectSNP Man page Source code
snpgdsSlidingWindow Man page Source code
snpgdsSummary Man page Source code
snpgdsTranspose Man page Source code
snpgdsVCF2GDS Man page Source code
snpgdsVCF2GDS_R Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllUtilities.R
R/Conversion.R
R/Conversion2.R
R/IBD.R
R/IBS.R
R/Internal.R
R/LD.R
R/PCA.R
README.md
build
build/vignette.rds
data
data/hapmap_geno.RData
inst
inst/CITATION
inst/doc
inst/doc/SNPRelateTutorial.R
inst/doc/SNPRelateTutorial.Rmd
inst/doc/SNPRelateTutorial.html
inst/extdata
inst/extdata/hapmap_geno.gds
inst/extdata/plinkhapmap.bed.gz
inst/extdata/plinkhapmap.bim.gz
inst/extdata/plinkhapmap.fam.gz
inst/extdata/sequence.vcf
inst/unitTests
inst/unitTests/test_Func.R
inst/unitTests/test_LD.R
inst/unitTests/test_Transpose.R
inst/unitTests/test_examples.R
inst/unitTests/test_rel.R
inst/unitTests/valid
inst/unitTests/valid/Validate.Beta.RData
inst/unitTests/valid/Validate.EIGMIX.RData
inst/unitTests/valid/Validate.IBS.RData
inst/unitTests/valid/Validate.KING.RData
inst/unitTests/valid/Validate.MoM.RData
inst/unitTests/valid/Validate.PCA.RData
man
man/SNPGDSFileClass-class.Rd
man/SNPRelate-package.Rd
man/hapmap_geno.Rd
man/snpgdsAdmixPlot.Rd
man/snpgdsAdmixProp.Rd
man/snpgdsAlleleSwitch.Rd
man/snpgdsApartSelection.Rd
man/snpgdsBED2GDS.Rd
man/snpgdsClose.Rd
man/snpgdsCombineGeno.Rd
man/snpgdsCreateGeno.Rd
man/snpgdsCreateGenoSet.Rd
man/snpgdsCutTree.Rd
man/snpgdsDiss.Rd
man/snpgdsDrawTree.Rd
man/snpgdsEIGMIX.Rd
man/snpgdsErrMsg.Rd
man/snpgdsExampleFileName.Rd
man/snpgdsFst.Rd
man/snpgdsGDS2BED.Rd
man/snpgdsGDS2Eigen.Rd
man/snpgdsGDS2PED.Rd
man/snpgdsGEN2GDS.Rd
man/snpgdsGRM.Rd
man/snpgdsGetGeno.Rd
man/snpgdsHCluster.Rd
man/snpgdsHWE.Rd
man/snpgdsIBDKING.Rd
man/snpgdsIBDMLE.Rd
man/snpgdsIBDMLELogLik.Rd
man/snpgdsIBDMoM.Rd
man/snpgdsIBDSelection.Rd
man/snpgdsIBS.Rd
man/snpgdsIBSNum.Rd
man/snpgdsIndInb.Rd
man/snpgdsIndInbCoef.Rd
man/snpgdsIndivBeta.Rd
man/snpgdsLDMat.Rd
man/snpgdsLDpair.Rd
man/snpgdsLDpruning.Rd
man/snpgdsOpen.Rd
man/snpgdsOption.Rd
man/snpgdsPCA.Rd
man/snpgdsPCACorr.Rd
man/snpgdsPCASNPLoading.Rd
man/snpgdsPCASampLoading.Rd
man/snpgdsPED2GDS.Rd
man/snpgdsPairIBD.Rd
man/snpgdsPairIBDMLELogLik.Rd
man/snpgdsPairScore.Rd
man/snpgdsSNPList.Rd
man/snpgdsSNPListClass.Rd
man/snpgdsSNPListIntersect.Rd
man/snpgdsSNPListStrand.Rd
man/snpgdsSNPRateFreq.Rd
man/snpgdsSampMissRate.Rd
man/snpgdsSelectSNP.Rd
man/snpgdsSlidingWindow.Rd
man/snpgdsSummary.Rd
man/snpgdsTranspose.Rd
man/snpgdsVCF2GDS.Rd
man/snpgdsVCF2GDS_R.Rd
src
src/ConvToGDS.cpp
src/Makevars
src/Makevars.win
src/R_SNPRelate.c
src/SNPRelate.cpp
src/ThreadPool.cpp
src/ThreadPool.h
src/dGenGWAS.cpp
src/dGenGWAS.h
src/dVect.cpp
src/dVect.h
src/genBeta.cpp
src/genEIGMIX.cpp
src/genFst.cpp
src/genHWE.cpp
src/genIBD.cpp
src/genIBS.cpp
src/genKING.cpp
src/genLD.cpp
src/genPCA.cpp
src/genPCA.h
src/genSlideWin.cpp
tests
tests/runTests.R
vignettes
vignettes/SNPRelate-Flowchart.png
vignettes/SNPRelateTutorial.Rmd
vignettes/link.png
SNPRelate documentation built on May 20, 2017, 9:15 p.m.

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