Genome-Wide Haplotyping


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Documentation for package ‘GHap’ version 2.0.0

Help Pages

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