cc.trans.probs: Transition probabilities for CC mice.

View source: R/transition.probs.R

cc.trans.probsR 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) 

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