get.trans.probs {DOQTL} | R Documentation

## 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).

### Author(s)

Daniel Gatti

### 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"))

[Package DOQTL version 1.19.0 Index]