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

hapmap_genoSNP genotypes of HapMap samples
snpgdsAdmixPlotPlot Ancestry Proportions
snpgdsAdmixPropEstimate ancestral proportions from the eigen-analysis
snpgdsApartSelectionSelect SNPs with a basepair distance
snpgdsBED2GDSConversion from PLINK BED to GDS
snpgdsCloseClose the SNP GDS File
snpgdsCombineGenoMerge SNP datasets
snpgdsCreateGenoCreate a SNP genotype dataset from a matrix
snpgdsCreateGenoSetCreate a SNP genotype dataset from a GDS file
snpgdsCutTreeDetermine clusters of individuals
snpgdsDissIndividual dissimilarity analysis
snpgdsDrawTreeDraw a dendrogram
snpgdsEIGMIXEigen-analysis on SNP genotype data
snpgdsErrMsgGet the last error information
snpgdsExampleFileNameExample GDS file
snpgdsFstF-statistics (fixation indices)
snpgdsGDS2BEDConversion from GDS to PLINK BED
snpgdsGDS2EigenConversion from GDS to Eigen (EIGENSTRAT)
snpgdsGDS2PEDConversion from GDS to PED
snpgdsGEN2GDSConversion from Oxford GEN format to GDS
snpgdsGetGenoTo get a genotype matrix
snpgdsGRMGenetic Relationship Matrix (GRM) for SNP genotype data
snpgdsHClusterHierarchical cluster analysis
snpgdsHWEStatistical test of Hardy-Weinberg Equilibrium
snpgdsIBDKINGKING method of moment for the identity-by-descent (IBD)...
snpgdsIBDMLEMaximum likelihood estimation (MLE) for the...
snpgdsIBDMLELogLikLog likelihood for MLE method in the Identity-By-Descent...
snpgdsIBDMoMPLINK method of moment (MoM) for the Identity-By-Descent...
snpgdsIBDSelectionGet a table of IBD coefficients
snpgdsIBSIdentity-By-State (IBS) proportion
snpgdsIBSNumIdentity-By-State (IBS)
snpgdsIndInbIndividual Inbreeding Coefficients
snpgdsIndInbCoefIndividual Inbreeding Coefficient
snpgdsIndivBetaIndividual inbreeding and relatedness estimation (beta...
snpgdsLDMatLinkage Disequilibrium (LD) analysis
snpgdsLDpairLinkage Disequilibrium (LD)
snpgdsLDpruningLinkage Disequilibrium (LD) based SNP pruning
snpgdsMergeGRMMerge Multiple Genetic Relationship Matrices (GRM)
snpgdsOpenOpen a SNP GDS File
snpgdsOptionOption settings: chromosome coding, etc
snpgdsPairIBDCalculate Identity-By-Descent (IBD) Coefficients
snpgdsPairIBDMLELogLikLog likelihood for MLE method in the Identity-By-Descent...
snpgdsPairScoreGenotype Score for Pairs of Individuals
snpgdsPCAPrincipal Component Analysis (PCA) on SNP genotype data
snpgdsPCACorrPC-correlated SNPs in principal component analysis
snpgdsPCASampLoadingProject individuals onto existing principal component axes
snpgdsPCASNPLoadingSNP loadings in principal component analysis
snpgdsPED2GDSConversion from PLINK PED to GDS
snpgdsSampMissRateMissing Rate of Samples
snpgdsSelectSNPSNP selection
snpgdsSlidingWindowSliding window
snpgdsSNPListCreate a SNP list object
snpgdsSNPListClassthe class of a SNP list
snpgdsSNPListIntersectGet a common SNP list between/among SNP list objects
snpgdsSNPRateFreqAllele Frequency, Minor Allele Frequency, Missing Rate of...
snpgdsSummarySummary of GDS genotype file
snpgdsTransposeTranspose genotypic matrix
snpgdsVCF2GDSReformat VCF file(s)
snpgdsVCF2GDS_RReformat a VCF file (R implementation)
SNPRelate-packageParallel Computing Toolset for Genome-Wide Association...
SNPRelate documentation built on Nov. 1, 2018, 3:35 a.m.