Genome-Wide Haplotyping


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Documentation for package ‘GHap’ version 1.2.1

Help Pages

ghap.ancestral Inference of haplotype origin
ghap.assoc Association analysis for HapAlleles and HapBlocks
ghap.blmm Bayesian linear mixed model
ghap.blockgen Haplotype block generator
ghap.blockstats Block statistics
ghap.blup Convert breeding values into BLUP solutions of HapAllele effects
ghap.fst Haplotype Fst
ghap.hap2tped Convert haplotype allele counts to PLINK tped
ghap.haplotyping Haplotype genotypes
ghap.hapstats Haplotype statistics
ghap.kinship Kinship matrix from haplotypes
ghap.lmm Frequentist linear mixed model
ghap.loadhaplo Load haplotype genotype data
ghap.loadphase Load phased genotype data
ghap.maf Compute marker minor allele frequencies
ghap.makefile Create example input files
ghap.mergehaplo Merging GHap.haplo objects
ghap.mergephase Merging GHap.phase objects
ghap.mme Mixed linear model solver
ghap.outhaplo Output GHap.haplo object to a file
ghap.outphase Output GHap.phase object to a file
ghap.pca Principal Components Analysis
ghap.profile Haplotype allele profile
ghap.simpheno Quantitative trait simulation using real HapGenotype data
ghap.subsethaplo Subset GHap.hapo object
ghap.subsetphase Subset GHap.phase object