hapdos2mrkdos: calculate the marker dosages resulting from haplotype dosage combinations

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

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

Details

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

Examples

Run this code

# NOT RUN {
# 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)
# }