locate_xo: Locate crossovers

In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

Locate crossovers

Description

Estimate the locations of crossovers in each individual on each chromosome.

Usage

locate_xo(geno, map, quiet = TRUE, cores = 1)

Arguments

geno	List of matrices of genotypes (output of maxmarg() or viterbi()).
map	List of vectors with the map positions of the markers.
quiet	If FALSE, print progress messages.
cores	Number of CPU cores to use, for parallel calculations. (If 0, use parallel::detectCores().) Alternatively, this can be links to a set of cluster sockets, as produced by parallel::makeCluster().

Value

A list of lists of estimated crossover locations, with crossovers placed at the midpoint of the intervals that contain them.

See Also

count_xo()

Examples

iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
map <- insert_pseudomarkers(iron$gmap, step=1)
pr <- calc_genoprob(iron, map, error_prob=0.002, map_function="c-f")
g <- maxmarg(pr)
pos <- locate_xo(g, iron$gmap)

qtl2 documentation built on May 29, 2024, 11:46 a.m.