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

In DOQTL: Genotyping and QTL Mapping in DO 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) 

DOQTL documentation built on May 6, 2019, 3:09 a.m.