interp_genoprob: Interpolate genotype probabilities

In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

Interpolate genotype probabilities

Description

Linear interpolation of genotype probabilities, mostly to get two sets onto the same map for comparison purposes.

Usage

interp_genoprob(probs, map, cores = 1)

Arguments

probs	Genotype probabilities, as calculated from calc_genoprob().
map	List of vectors of map positions.
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().

Details

We reduce probs to the positions present in map and then interpolate the genotype probabilities at additional positions in map by linear interpolation using the two adjacent positions. Off the ends, we just copy over the first or last value unchanged.

In general, it's better to use insert_pseudomarkers() and calc_genoprob() to get genotype probabilities at additional positions along a chromosome. This function is a very crude alternative that was implemented in order to compare genotype probabilities derived by different methods, where we first need to get them onto a common set of positions.

Value

An object of class "calc_genoprob", like the input, but with additional positions present in map. See calc_genoprob().

See Also

calc_genoprob()

Examples

iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))

probs <- calc_genoprob(iron, iron$gmap, error_prob=0.002)

# you generally wouldn't want to do this, but this is an illustration
map <- insert_pseudomarkers(iron$gmap, step=1)
probs_map <- interp_genoprob(probs, map)

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