hapdos2hapcomb: convert haplotype dosages to haplotype combinations

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

Description

convert a vector or matrix of haplotype dosages to a vector or matrix of haplotype combinations

Usage

hapdos2hapcomb(hapdos, ploidy)

Arguments

hapdos

a vector with one item for some or all possible haplotypes, with the dosage of the haplotypes, summing to ploidy; or a matrix where each column is such a vector, each representing an individual. Missing data are allowed (but any NA makes the entire vector or matrix column unknown); if a matrix, 0 rows indicate missing values for all individuals. When hapdos is a matrix, the haplotype numbers must be given as rownames; when a vector, as names. Not all possible haplotype numbers need to be present but the ones that are present must be in ascending order, no duplicates or missing values allowed.

ploidy

the ploidy (one number)

Value

a sorted vector of length ploidy with all haplotype numbers present, or a matrix where each column is such a vector, with the same colnames as hapdos

Examples

# specify haplotype dosages of 4 tetraploid individuals,
# only the 3 occurring haplotypes (1, 5 and 6) are given:
haplodosg <- matrix(c(1,2,1, 4,0,0, 0,4,0, 0,0,4), nrow=3,
                   dimnames=list(paste0("demohap_", c(1,5,6)), paste0("indiv", 1:4)))
# usage with hapdos as matrix:
hapdos2hapcomb(hapdos=haplodosg, ploidy=4)
# usage with hapdos as vector:
hapdos2hapcomb(hapdos=haplodosg[, 1], ploidy=4)

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