lodLinkage: Test for linkage

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Test for linkage

Description

Computes the LOD score(s) given recombination fraction(s) as well as number of non-recombinants and recombinants, testing for "ref.frac = 0".

Usage

lodLinkage(rec.frac, nb.nonrec, nb.rec)

Arguments

rec.frac	vector of recombination fraction(s); if above 0.5, will use 1 - rec.frac; will be recycled to match nb.nonrec and nb.rec
nb.nonrec	vector of number(s) of non-recombinant offsprings; will be recycled to match rec.frac
nb.rec	vector of number(s) of recombinant offsprings; will be recycled to match rec.frac

Value

vector of LOD score(s)

Author(s)

Timothee Flutre

Examples

## Not run: ## from "Genetic map construction with R/qtl" by Karl Broman (2012)
## page 10: http://www.rqtl.org/tutorials/geneticmaps.pdf
n <- 300
nb.rec <- 27 + 27
nb.nonrec <- 300 - nb.rec
(est.rec.frac <- nb.rec / n) # estimator for a backcross; 0.18
lodLinkage(est.rec.frac, nb.nonrec, nb.rec) # ~28.9

## show how input rec.frac is recycled
lodLinkage(seq(0, 0.5, 0.05), nb.nonrec, nb.rec)
plot(lodLinkage(seq(0, 0.5, 0.05), nb.nonrec, nb.rec), type="b",
     xlab="recombination fraction", ylab="LOD score", las=1)

## show how inputs nb.nonrec and nb.rec are recycled
lodLinkage(est.rec.frac, n - 60, 60)
lodLinkage(est.rec.frac, c(n - 54, n - 60), c(54, 60))

## End(Not run)

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.