get.ril.prob: Calculate the haplotype probabilities for an RIL chromosome

In kbroman/ricalc: Calculations for Recombinant Inbred Lines

Calculate the haplotype probabilities for an RIL chromosome

Description

Calculate (numerically) the haplotype probabilities on a 2- or 4-way RIL chromosome.

Usage

get.ril.prob(r, coinc=1, n.strains=c("2","4"), type=c("selfing","sibmating"),
         chrtype=c("A","X"), n.loci=c("2","3"), verbose=TRUE)

Arguments

r	Recombination fraction between markers.
coinc	The 3-point coincidence (used only when n.loci=3).
n.strains	Number of parental strains.
type	Method for mating.
chrtype	Indicates autosome or X chromosome (when type=sibmating only).
n.loci	Number of loci.
verbose	If TRUE, print stuff as things progress.

Value

A vector of probabilities, with absorbing states in their reduced form.

Author(s)

Karl W Broman, [e-mail]

References

Haldane, J. B. S. and Waddington, C. H. (1931) Inbreeding and linkage. Genetics 16, 357–374.

Broman, K. W. (2005) The genomes of recombinant inbred lines. Genetics 169, 1133–1146.

See Also

get.ril.coinc

kbroman/ricalc documentation built on May 17, 2023, 11:54 p.m.