smooth_gmap {qtl2}

Smooth genetic map

Description

Smooth a genetic map by mixing it with a bit of constant recombination (using a separate recombination rate for each chromosome), to eliminate intervals that have exactly 0 recombination.

Usage

smooth_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 (1-\alpha)d_g + \alpha d_p r where r = L_g / L_p is the chromosome-specific recombination rate.

Value

A genetic map like the input gmap, but smoothed by mixing it with a proportion alpha of constant recombination on each chromosome.

See Also

unsmooth_gmap()

Examples

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