do.trans.probs {DOQTL} | R Documentation

## 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)

[Package DOQTL version 1.18.0 Index]