do.trans.probs: Determine DO transition probabilities

In dmgatti/DOQTL: Genotyping and QTL Mapping in DO Mice

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.

Details

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

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).

Author(s)

Daniel Gatti and Karl Broman

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) 

dmgatti/DOQTL documentation built on April 7, 2024, 10:35 p.m.