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