# Genome-Wide Haplotyping

## Documentation for package ‘GHap’ version 1.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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