SNPRelate: Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)

A High-performance computing toolset for relatedness and principal component analysis of SNP data

AuthorXiuwen Zheng
Date of publication2014-09-12 21:44:05
MaintainerXiuwen Zheng <zhengx@u.washington.edu>
LicenseGPL-3
Version0.9.19
http://corearray.sourceforge.net/

View on R-Forge

Man pages

hapmap_geno: SNP genotypes of HapMap samples

snpgdsBED2GDS: Conversion from PLINK BED to GDS

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

snpgdsErrMsg: Get the last error information

snpgdsExampleFileName: Example GDS file

snpgdsGDS2BED: Conversion from GDS to PLINK BED

snpgdsGDS2Eigen: Conversion from GDS to Eigen (EIGENSTRAT)

snpgdsGDS2PED: Conversion from GDS to PED

snpgdsGetGeno: To get a genotype matrix

snpgdsHCluster: Hierarchical cluster analysis

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: The numbers of Identity-By-State (IBS) SNPs

snpgdsIndInb: Individual Inbreeding Coefficients

snpgdsIndInbCoef: Individual Inbreeding Coefficient

snpgdsLDMat: Linkage Disequilibrium (LD) analysis

snpgdsLDpair: Linkage Disequilibrium (LD)

snpgdsLDpruning: Linkage Disequilibrium (LD) based SNP pruning

snpgdsOption: Option settings: chromosome coding, etc

snpgdsPairIBD: Calculate Identity-By-Descent (IBD) Coefficients

snpgdsPairIBDMLELogLik: Log likelihood for MLE method in the Identity-By-Descent...

snpgdsPCA: Principal Component Analysis (PCA) on SNP genotype data

snpgdsPCACorr: SNP correlation in principal component analysis

snpgdsPCASampLoading: Project individuals onto existing principal component axes

snpgdsPCASNPLoading: SNP loadings in principal component analysis

snpgdsSampMissrate: Missing Rate of Samples

snpgdsSelectSNP: SNP selection

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

snpgdsVCF2GDS: Reformat a VCF file

SNPRelate-package: Parallel Computing Toolset for genome-wide association...

Functions

hapmap_geno Man page
snpgdsBED2GDS Man page
snpgdsCombineGeno Man page
snpgdsCreateGeno Man page
snpgdsCreateGenoSet Man page
snpgdsCutTree Man page
snpgdsDiss Man page
snpgdsDrawTree Man page
snpgdsErrMsg Man page
snpgdsExampleFileName Man page
snpgdsGDS2BED Man page
snpgdsGDS2Eigen Man page
snpgdsGDS2PED Man page
snpgdsGetGeno Man page
snpgdsHCluster Man page
snpgdsIBDKING Man page
snpgdsIBDMLE Man page
snpgdsIBDMLELogLik Man page
snpgdsIBDMoM Man page
snpgdsIBDSelection Man page
snpgdsIBS Man page
snpgdsIBSNum Man page
snpgdsIndInb Man page
snpgdsIndInbCoef Man page
snpgdsLDMat Man page
snpgdsLDpair Man page
snpgdsLDpruning Man page
snpgdsOption Man page
snpgdsPairIBD Man page
snpgdsPairIBDMLELogLik Man page
snpgdsPCA Man page
snpgdsPCACorr Man page
snpgdsPCASampLoading Man page
snpgdsPCASNPLoading Man page
snpgdsSampMissrate Man page
snpgdsSelectSNP Man page
snpgdsSNPList Man page
snpgdsSNPListClass Man page
snpgdsSNPListIntersect Man page
snpgdsSNPListStrand Man page
snpgdsSNPRateFreq Man page
snpgdsSummary Man page
snpgdsVCF2GDS Man page
SNPRelate Man page
SNPRelate-package Man page

Files

SNPRelate/DESCRIPTION
SNPRelate/NAMESPACE
SNPRelate/NEWS
SNPRelate/R
SNPRelate/R/IBD.r
SNPRelate/R/IBS.r
SNPRelate/R/LD.r
SNPRelate/R/PCA.r
SNPRelate/R/SNPRelate_Main.r
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.Rnw
SNPRelate/inst/doc/SNPRelateTutorial.pdf
SNPRelate/inst/extdata
SNPRelate/inst/extdata/hapmap_geno.gds
SNPRelate/inst/extdata/plinkhapmap.bed
SNPRelate/inst/extdata/plinkhapmap.bim
SNPRelate/inst/extdata/plinkhapmap.fam
SNPRelate/inst/extdata/sequence.vcf
SNPRelate/inst/unitTests
SNPRelate/inst/unitTests/runTests.R
SNPRelate/inst/unitTests/runit.IBS.r
SNPRelate/inst/unitTests/runit.PCA.r
SNPRelate/inst/unitTests/runit.PLINK.r
SNPRelate/inst/unitTests/valid
SNPRelate/inst/unitTests/valid/Validate.IBS.RData
SNPRelate/inst/unitTests/valid/Validate.MoM.RData
SNPRelate/inst/unitTests/valid/Validate.PCA.RData
SNPRelate/man
SNPRelate/man/SNPRelate-package.Rd SNPRelate/man/hapmap_geno.Rd SNPRelate/man/snpgdsBED2GDS.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/snpgdsErrMsg.Rd SNPRelate/man/snpgdsExampleFileName.Rd SNPRelate/man/snpgdsGDS2BED.Rd SNPRelate/man/snpgdsGDS2Eigen.Rd SNPRelate/man/snpgdsGDS2PED.Rd SNPRelate/man/snpgdsGetGeno.Rd SNPRelate/man/snpgdsHCluster.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/snpgdsLDMat.Rd SNPRelate/man/snpgdsLDpair.Rd SNPRelate/man/snpgdsLDpruning.Rd SNPRelate/man/snpgdsOption.Rd SNPRelate/man/snpgdsPCA.Rd SNPRelate/man/snpgdsPCACorr.Rd SNPRelate/man/snpgdsPCASNPLoading.Rd SNPRelate/man/snpgdsPCASampLoading.Rd SNPRelate/man/snpgdsPairIBD.Rd SNPRelate/man/snpgdsPairIBDMLELogLik.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/snpgdsSummary.Rd SNPRelate/man/snpgdsVCF2GDS.Rd
SNPRelate/src
SNPRelate/src/CoreDEF.h
SNPRelate/src/CoreGDSLink.cpp
SNPRelate/src/CoreGDSLink.h
SNPRelate/src/Makevars
SNPRelate/src/Makevars.win
SNPRelate/src/SNPRelate.cpp
SNPRelate/src/dGWASMath.h
SNPRelate/src/dGenGWAS.cpp
SNPRelate/src/dGenGWAS.h
SNPRelate/src/dType.h
SNPRelate/src/dVect.cpp
SNPRelate/src/dVect.h
SNPRelate/src/genIBD.cpp
SNPRelate/src/genIBS.cpp
SNPRelate/src/genLD.cpp
SNPRelate/src/genPCA.cpp
SNPRelate/tests
SNPRelate/tests/runTests.R
SNPRelate/vignettes
SNPRelate/vignettes/SNPRelate-Flowchart.png
SNPRelate/vignettes/SNPRelateTutorial-IBDMLE.png
SNPRelate/vignettes/SNPRelateTutorial.Rnw

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