unsmooth_gmap: Unsmooth genetic map

In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

Unsmooth genetic map

Description

Performs the reverse operation of smooth_gmap(), in case one wants to go back to the original genetic map.

Usage

unsmooth_gmap(gmap, pmap, alpha = 0.02)

Arguments

gmap	Genetic map, as a list of numeric vectors; each vector gives marker positions for a single chromosome.
pmap	Physical map, as a list of numeric vectors; each vector gives marker positions for a single chromosome, with the same chromosomes and markers as gmap.
alpha	Proportion of mixture to take from constant recombination.

Details

An interval of genetic length d_g and physical length d_p is changed to have length (d_g - \alpha d_p r)/(1-\alpha) where r = L_g / L_p is the chromosome-specific recombination rate.

Value

A genetic map like the input gmap, but with the reverse operation of smooth_gmap() applied, provided that exactly the same physical map and alpha are used.

See Also

smooth_gmap()

Examples

iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
gmap_adj <- smooth_gmap(iron$gmap, iron$pmap)
gmap_back <- unsmooth_gmap(gmap_adj, iron$pmap)

qtl2 documentation built on April 22, 2023, 1:10 a.m.