DOQTL (version 1.8.0)

do.trans.probs: Determine DO transition probabilities

Description

Determine the genotype state transition probability for DO mice of a specific generation between all of the markers on a given chromosome.

Usage

do.trans.probs(states, snps, chr = c(1:19, "X"), sex = c("M", "F"), do.gen)

Arguments

states

Character vector of possible genotype states.

snps

Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively.

chr

Character containing the chromosome for which transition probabilities should be calculated.

sex

Character that is one of FALSE or M, indicating the sex to use on the X chromosome.

do.gen

Number vector indicating the DO outbreeding generations to calculate.

Value

List containing one element per unique DO generation supplied in the do.gen argument. Each list element contains a 3 dimensional array of transition probabilities between each pair of markers (num.states by num.states by num.markers - 1).

Details

This function is used to calculate the transition probabilities between markers for different DO outbreeding generations.

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:  do.trans.probs(states, snps, chr = c(1:19, "X"), sex = c("M", F), do.gen)