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

hapmap_genoSNP genotypes of HapMap samples
snpgdsBED2GDSConversion from PLINK BED to GDS
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
snpgdsErrMsgGet the last error information
snpgdsExampleFileNameExample GDS file
snpgdsGDS2BEDConversion from GDS to PLINK BED
snpgdsGDS2EigenConversion from GDS to Eigen (EIGENSTRAT)
snpgdsGDS2PEDConversion from GDS to PED
snpgdsGetGenoTo get a genotype matrix
snpgdsHClusterHierarchical cluster analysis
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
snpgdsIBSNumThe numbers of Identity-By-State (IBS) SNPs
snpgdsIndInbIndividual Inbreeding Coefficients
snpgdsIndInbCoefIndividual Inbreeding Coefficient
snpgdsLDMatLinkage Disequilibrium (LD) analysis
snpgdsLDpairLinkage Disequilibrium (LD)
snpgdsLDpruningLinkage Disequilibrium (LD) based SNP pruning
snpgdsOptionOption settings: chromosome coding, etc
snpgdsPairIBDCalculate Identity-By-Descent (IBD) Coefficients
snpgdsPairIBDMLELogLikLog likelihood for MLE method in the Identity-By-Descent...
snpgdsPCAPrincipal Component Analysis (PCA) on SNP genotype data
snpgdsPCACorrSNP correlation in principal component analysis
snpgdsPCASampLoadingProject individuals onto existing principal component axes
snpgdsPCASNPLoadingSNP loadings in principal component analysis
snpgdsSampMissrateMissing Rate of Samples
snpgdsSelectSNPSNP selection
snpgdsSNPListCreate a SNP list object
snpgdsSNPListClassthe class of a SNP list
snpgdsSNPListIntersectGet a common SNP list between two SNP list objects
snpgdsSNPListStrandSwitch allele strand.
snpgdsSNPRateFreqAllele Frequency, Minor Allele Frequency, Missing Rate of...
snpgdsSummarySummary of GDS genotype file
snpgdsVCF2GDSReformat a VCF file
SNPRelate-packageParallel Computing Toolset for genome-wide association...
SNPRelate documentation built on May 2, 2019, 4:56 p.m.