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 |