hapcomb2hapdos: convert haplotype combinations to haplotype dosages

In PolyHaplotyper: Assignment of Haplotypes Based on SNP Dosages in Diploids and Polyploids

Description

converts matrices that contain haplotype combinations in columns (as the matrices in ahccompletelist or ahclist) to matrices with the haplotype dosages

Usage

hapcomb2hapdos(hapcomb, nhap)

Arguments

hapcomb	matrix with <ploidy> rows and any number of columns. Each column contains a set of haplotypes (numbers in 1 ... nhap). NAs allowed but no values outside this range (not checked). E.g. a column with numbers 1-1-3-12 means two copies of haplotype 1 and one of haplotypes 3 and 12 each.
nhap	the total number of possible haplotypes: 2^nmrk where nmrk is the number of bi-allelic markers in the haploblock

Value

matrix with nhap rows (one row for each possible haplotype) and as many columns as in hapmat, giving the dosages of each haplotype in each column of hapmat.

Examples

# specify haplotype combinations of 2 individuals:
haplocomb <- matrix(c(1,5,5,6, 5,6,6,6), ncol=2,
                   dimnames=list(NULL, c("indiv1", "indiv2")))
# convert to dosage matrix,
# assuming haploblock has 3 markers, so 8 possible haplotypes:
hapcomb2hapdos(hapcomb=haplocomb, nhap=8)

PolyHaplotyper documentation built on June 17, 2021, 5:12 p.m.