getGameteFreqs: get all gametes and their frequencies for a parental...

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

Description

get all gametes and their frequencies for a parental haplotype combination

Usage

getGameteFreqs(parhac, DRrate)

Arguments

parhac	vector of the parental haplotype combination of length <ploidy>, giving the <ploidy> haplotype numbers present per haplotype giving the dosage of that haplotype, summing to ploidy
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)

Details

for hexaploids the DR gametes consist of a duplication of one of the 6 parental alleles, combined with one copy of one of the other 5 alleles.
Calculation is faster if DRrate is 0.0

Value

a list of 2 elements:
hapcomb: a matrix with one column per unique gamete and ploidy/2 rows. Each element is the number (ID) of a haplotype). Within columns the haplotypes are sorted from low to high; the columns are ordered from left to right, first on row 1, then on row 2 etc
freq: a vector of length ncol(hapcomb), with for each gamete in hapcomb its frequency (0.0 ... 1.0)

Examples

# specify combination of haplotypes in a tetraploid parent:
hapcomb <- c(2,2,5,6) # 2 copies of haplotype 2, 1 each of 5 and 6
# gamete frequencies without double reduction:
getGameteFreqs(parhac=hapcomb, DRrate=0)
# gamete frequencies with 5\% double reduction:
getGameteFreqs(parhac=hapcomb, DRrate=0.05)

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