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

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

Author
Xiuwen Zheng
Date of publication
2014-09-12 21:44:05
Maintainer
Xiuwen Zheng <zhengx@u.washington.edu>
License
GPL-3
Version
0.9.19
URLs

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