DOQTL (version 1.8.0)

get.trans.probs: Get the transition probabilities between markers.

Description

Based on the DO founders and the recombination fraction, calculate the transition probability between markers on one chromosome.

Usage

get.trans.probs(r, do.gen, alpha, chr = c(1:19, "X"), sex = c("M", "F"))

Arguments

r

Double vector of recombination fractions between SNPs.

do.gen

Integer containing the outbreeding generation of DO.

alpha

Double vector, proportion of preCC progenitors at generation k. Generation numbers in the names.

chr

Character, one of 1:19, X.

sex

Character, either M or FALSE. Only used on X chromosome.

Value

Numeric three dimensional array of transition probabilities between each pair of markers (num.states by num.states by num.markers - 1).

References

Haplotype probabilities in advanced intercross populations. Broman KW. G3 (Bethesda). 2012 FALSEeb;2(2):199-202. doi: 10.1534/g3.111.001818. Epub 2012 FALSEeb 1. PMID: 22384398 Genotype probabilities at intermediate generations in the construction of recombinant inbred lines. Broman KW. Genetics. 2012 FALSEeb;190(2):403-12. doi: 10.1534/genetics.111.132647. PMID: 22345609

Examples

  ## Not run:  get.trans.probs(r, do.gen, alpha, chr = c(1:19, "X"), sex = c("M", "F"))