SNPGDSFileClass         SNPGDSFileClass
SNPRelate-package       Parallel Computing Toolset for Genome-Wide
                        Association Studies
hapmap_geno             SNP genotypes of HapMap samples
snpgdsAdmixPlot         Plot Ancestry Proportions
snpgdsAdmixProp         Estimate ancestral proportions from the
                        eigen-analysis
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
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
snpgdsGRM               Genetic Relationship Matrix (GRM) for SNP
                        genotype data
snpgdsGetGeno           To get a genotype matrix
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
snpgdsMergeGRM          Merge Multiple Genetic Relationship Matrices
                        (GRM)
snpgdsOpen              Open a SNP GDS File
snpgdsOption            Option settings: chromosome coding, etc
snpgdsPCA               Principal Component Analysis (PCA) on SNP
                        genotype data
snpgdsPCACorr           PC-correlated SNPs in principal component
                        analysis
snpgdsPCASNPLoading     SNP loadings in principal component analysis
snpgdsPCASampLoading    Project individuals onto existing principal
                        component axes
snpgdsPED2GDS           Conversion from PLINK PED to GDS
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
snpgdsSNPList           Create a SNP list object
snpgdsSNPListClass      the class of a SNP list
snpgdsSNPListIntersect
                        Get a common SNP list between/among SNP list
                        objects
snpgdsSNPRateFreq       Allele Frequency, Minor Allele Frequency,
                        Missing Rate of SNPs
snpgdsSampMissRate      Missing Rate of Samples
snpgdsSelectSNP         SNP selection
snpgdsSlidingWindow     Sliding window
snpgdsSummary           Summary of GDS genotype file
snpgdsTranspose         Transpose genotypic matrix
snpgdsVCF2GDS           Reformat VCF file(s)
snpgdsVCF2GDS_R         Reformat a VCF file (R implementation)
