haplotypeToGenotype: Call Genotypes from Haplotype Data

In bahlolab/isoRelate: Identity-by-Descent Inference of Haploid Recombining Organisms

Description

haplotypeToGenotype transforms PLINK haplotype data into genotype data of the form -1, 0, 1 and 2 representing missing genotypes, homozygous reference, heterozygous and homozygous alternative respectively. Haploid isolates are coded as diploid although will not have heterozygous genotypes.

Usage

haplotypeToGenotype(haplotypes, moi)

Arguments

haplotypes	An integer matrix of haplotype data in PLINK format. A allele is denoted 1, B allele is denoted 2 and missing data is denoted 0
moi	An integer vector of multiplicity of infection (MOI) estimates for each isoalte. Isolate MOI estimates should be ordered such that value n of moi corresponds to column n of haplotypes.

Value

A matrix with genotype calls where columns correspond to isolates and rows correspond to SNPs

bahlolab/isoRelate documentation built on May 11, 2019, 5:25 p.m.