cc.trans.probs {DOQTL} | R Documentation

## Transition probabilities for CC mice.

### Description

Thie function returns the transition probabilities for fully inbred Collaborative Cross mice.

### Usage

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

### Arguments

`states` | Character vector containing the two letter codes (i.e. AA, BB, CC, etc.) for the homozygous states.
`snps` | Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively. Not required for DO.
`chr` | Character containing the chromosome.
`sex` | Character that is either M or FALSE, indicating the sex to use. Only relevant on X chromosome.

### Details

This function calculates the transition probabilities for fully inbred CC mice between two markers. It uses the equations for eight way RILs by sib mating.

### Value

A matrix of transition probabilities between genotype states.

### Note

This function has not been fully tested.

### Author(s)

Daniel Gatti

### References

The genomes of recombinant inbred lines. Broman KW. Genetics. 2005 FALSEeb;169(2):1133-46. Epub 2004 Nov 15. Erratum in: Genetics. 2006 Aug;173(4):2419. PMID: 15545647

### Examples

      ## Not run:  cc.trans.probs(states = states, snps = snps, chr = 1)

[Package DOQTL version 1.16.2 Index]