hapdos2mrkdos: calculate the marker dosages resulting from haplotype dosage...

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

Description

calculate the marker dosages resulting from haplotype dosage combinations

Usage

hapdos2mrkdos(hapdos, allhap)

Arguments

hapdos	a matrix with one column per combination of haplotypes and one row for each possible haplotype (corresponding to the rows of allhap) with dosage of the haplotypes in each combination. A vector is interpreted as a one-column matrix; all columns must sum to ploidy. The rownames of the matrix (or names of the vector) must contain the haplotype numbers
allhap	a matrix as returned by allHaplotypes

Details

if hapdos contains NA values, all values in the corresponding column of the result will also be NA

Value

a matrix with columns corresponding to the columns of hapdos and one row for each marker, with the dosages of each marker in each combination; colnames are the mrkdids (marker dosage IDs), rownames are the marker names taken from allhap

Examples

# get a matrix of all haplotypes with the 3 specified markers:
ah <- allHaplotypes(mrknames=c("mrkA", "mrkB", "mrkC"))
# 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)))
# calculate the corresponding marker (SNP) dosages:
hapdos2mrkdos(hapdos=haplodosg, allhap=ah)

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