getFSfreqs: get all FS haplotype combinations expected from two parental...

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

Description

get all FS haplotype combinations expected from two parental haplotype combinations, with their frequencies. Different from getFScombs in that it returns the unique FS combinations as well as their frequencies, and that it also considers Double Reduction

Usage

getFSfreqs(parhac, DRrate)

Arguments

parhac	matrix with one column for each parent and <ploidy> rows, giving the haplotype combinations for each parent
DRrate	the rate of double reduction per meiosis (NOT per allele!); e.g. with a DRrate of 0.04, a tetraploid parent with genotype ABCD will produce a fraction of 0.04 of DR gametes AA, BB, CC and DD (each with a frequency of 0.01), and a fraction of 0.96 of the non-DR gametes AB, AC, AD, BC, BD, CD (each with a frequency of 0.16)

Value

a list of 2 elements:
FShac: a matrix with one column per unique FS haplotype combination and the same row count as parhac, giving the FS haplotype combinations. There are no duplicated columns but several (not necessarily adjacent) columns may correspond to the same mrkdid
freq: a vector of length ncol(hapcomb), with for each FS haplotype combination in hapcomb its frequency (0.0 ... 1.0). The colnames are NULL: haplotype combinations are not named.

Examples

# specify combinations of haplotypes in two tetraploid parents:
hapcomb <- matrix(c(2,2,5,6, 1,2,5,5), ncol=2)
# FS frequencies without double reduction:
getFSfreqs(parhac=hapcomb, DRrate=0)
# FS frequencies with 5\% double reduction:
getFSfreqs(parhac=hapcomb, DRrate=0.05)

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