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              Association analysis for HapAlleles
ghap.blockgen           Haplotype block generator
ghap.blockstats         HapBlock statistics
ghap.blup               Convert breeding values into BLUP solutions of
                        HapAllele effects
ghap.compress           Compress phased genotype data
ghap.fast2phase         Convert fastPHASE data into the GHap phase
                        format
ghap.freq               Compute marker allele frequencies
ghap.fst                Haplotype-based Fst
ghap.hap2plink          Convert haplotype allele counts to PLINK binary
ghap.haplotyping        Haplotype genotypes
ghap.hapstats           Haplotype allele statistics
ghap.hslice             Get a slice of the haplo object
ghap.karyoplot          Individual chromosome painting
ghap.kinship            Kinship matrix from haplotypes
ghap.kinv               Inverse of kinship matrix
ghap.lmm                Linear mixed model
ghap.loadhaplo          Load haplotype genotype data
ghap.loadphase          Load binary phased genotype data
ghap.makefile           Create example input files
ghap.manhattan          Manhattan plot
ghap.oxford2phase       Convert Oxford data into GHap phase
ghap.pca                Principal Components Analysis
ghap.profile            Haplotype allele profile
ghap.pslice             Get a slice of the phase object
ghap.simpheno           Quantitative trait simulation using real
                        HapGenotype data
ghap.subsethaplo        Subset GHap.hapo object
ghap.subsetphase        Subset GHap.phase object
ghap.vcf2phase          Convert VCF data into GHap phase
