qtl2 (version 0.24)

locate_xo: 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

# NOT RUN {
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)

# }