ghap.anc2plink          Convert ancestry tracks to PLINK binary
ghap.ancmark            Per marker ancestry proportions
ghap.ancplot            Barplot of predictions of ancestry proportions
ghap.ancsmooth          Smoothing of haplotype ancestry predictions
ghap.ancsvm             SVM-based predictions of haplotype ancestry
ghap.anctest            Prediction of haplotype ancestry
ghap.anctrain           Construction of prototype alleles
ghap.assoc              Genome-wide association analysis
ghap.blockgen           Haplotype block generator
ghap.blockstats         HapBlock statistics
ghap.compress           Compress phased genotype data
ghap.exfiles            Example files
ghap.fast2phase         Convert fastPHASE data into the GHap phase
                        format
ghap.freq               Compute marker allele frequencies
ghap.froh               Calculation of genomic inbreeding (FROH)
ghap.fst                Haplotype-based Fst
ghap.getHinv            Compute the inverse of H
ghap.hap2plink          Convert haplotype allele counts to PLINK binary
ghap.haplotyping        Haplotype genotypes
ghap.hapstats           Haplotype allele statistics
ghap.ibd                Estimation of IBD sharing
ghap.inbcoef            Compute measures of inbreeding
ghap.karyoplot          Individual chromosome painting
ghap.kinship            Relationship matrix based on genomic data
ghap.lmm                Linear mixed model
ghap.loadhaplo          Load haplotype genotype data
ghap.loadphase          Load binary phased genotype data
ghap.loadplink          Load binary PLINK data
ghap.makefile           Create example input files
ghap.manhattan          Manhattan plot
ghap.oxford2phase       Convert Oxford data into GHap phase
ghap.pedcheck           Summary statistics for pedigree
ghap.phase2plink        Export phase object to PLINK binary
ghap.predictblup        Predict BLUP from reference
ghap.profile            Genomic profile
ghap.relfind            Find relatives in IBD estimates
ghap.remlci             Confidence intervals for functions of variance
                        components
ghap.roh                Detection of runs of homozygosity (ROH)
ghap.simadmix           Simulate individuals from specified admixture
                        proportions
ghap.simmating          Simulate individuals from specified matings
ghap.simpheno           Quantitative trait simulation using real
                        genotype data
ghap.slice              Get a slice of a GHap object
ghap.subset             Subset GHap objects
ghap.varblup            Convert BLUP of individuals into BLUP of
                        variants
ghap.vcf2phase          Convert VCF data into GHap phase
