| SNPRelate-package | Parallel Computing Toolset for Genome-Wide Association Studies |
| hapmap_geno | SNP genotypes of HapMap samples |
| plot.snpgdsEigMixClass | Eigen-analysis on SNP genotype data |
| plot.snpgdsPCAClass | Principal Component Analysis (PCA) on SNP genotype data |
| snpgdsAdmixPlot | Plot Ancestry Proportions |
| snpgdsAdmixProp | Estimate ancestral proportions from the eigen-analysis |
| snpgdsAdmixTable | Plot Ancestry Proportions |
| snpgdsAlleleSwitch | Allele-switching |
| snpgdsApartSelection | Select SNPs with a basepair distance |
| snpgdsBED2GDS | Conversion from PLINK BED to GDS |
| snpgdsClose | Close the SNP GDS File |
| 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 |
| snpgdsEIGMIX | Eigen-analysis on SNP genotype data |
| snpgdsErrMsg | Get the last error information |
| snpgdsExampleFileName | Example GDS file |
| SNPGDSFileClass | SNPGDSFileClass |
| SNPGDSFileClass-class | SNPGDSFileClass |
| snpgdsFst | F-statistics (fixation indices) |
| snpgdsGDS2BED | Conversion from GDS to PLINK BED |
| snpgdsGDS2Eigen | Conversion from GDS to Eigen (EIGENSTRAT) |
| snpgdsGDS2PED | Conversion from GDS to PED |
| snpgdsGEN2GDS | Conversion from Oxford GEN format to GDS |
| snpgdsGetGeno | To get a genotype matrix |
| snpgdsGRM | Genetic Relationship Matrix (GRM) for SNP genotype data |
| snpgdsHCluster | Hierarchical cluster analysis |
| snpgdsHWE | Statistical test of Hardy-Weinberg Equilibrium |
| snpgdsIBDKING | KING method of moment for the identity-by-descent (IBD) analysis |
| snpgdsIBDMLE | Maximum likelihood estimation (MLE) for the Identity-By-Descent (IBD) Analysis |
| snpgdsIBDMLELogLik | Log likelihood for MLE method in the Identity-By-Descent (IBD) Analysis |
| snpgdsIBDMoM | PLINK method of moment (MoM) for the Identity-By-Descent (IBD) Analysis |
| snpgdsIBDSelection | Get a table of IBD coefficients |
| snpgdsIBS | Identity-By-State (IBS) proportion |
| snpgdsIBSNum | Identity-By-State (IBS) |
| snpgdsIndInb | Individual Inbreeding Coefficients |
| snpgdsIndInbCoef | Individual Inbreeding Coefficient |
| snpgdsIndivBeta | Individual inbreeding and relatedness estimation (beta estimator) |
| snpgdsLDMat | Linkage Disequilibrium (LD) analysis |
| snpgdsLDpair | Linkage Disequilibrium (LD) |
| snpgdsLDpruning | Linkage Disequilibrium (LD) based SNP pruning |
| snpgdsOpen | Open a SNP GDS File |
| snpgdsOption | Option settings: chromosome coding, etc |
| snpgdsPairIBD | Calculate Identity-By-Descent (IBD) Coefficients |
| snpgdsPairIBDMLELogLik | Log likelihood for MLE method in the Identity-By-Descent (IBD) Analysis |
| snpgdsPairScore | Genotype Score for Pairs of Individuals |
| snpgdsPCA | Principal Component Analysis (PCA) on SNP genotype data |
| snpgdsPCACorr | PC-correlated SNPs in principal component analysis |
| snpgdsPCASampLoading | Project individuals onto existing principal component axes |
| snpgdsPCASNPLoading | SNP loadings in principal component analysis |
| snpgdsPED2GDS | Conversion from PLINK PED to GDS |
| snpgdsSampMissRate | Missing Rate of Samples |
| snpgdsSelectSNP | SNP selection |
| snpgdsSlidingWindow | Sliding window |
| 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 SNPs |
| snpgdsSummary | Summary of GDS genotype file |
| snpgdsTranspose | Transpose genotypic matrix |
| snpgdsVCF2GDS | Reformat VCF file(s) |
| snpgdsVCF2GDS_R | Reformat a VCF file (R implementation) |
| SNPRelate | Parallel Computing Toolset for Genome-Wide Association Studies |