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...

Files in this package

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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