calc_het: Calculate heterozygosities
In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

calc_het

R Documentation

Calculate heterozygosities

Description

Calculate heterozygosites, by individual or by marker

Usage

calc_het(probs, by = c("individual", "marker"), omit_x = TRUE, cores = 1)

Arguments

`probs`	List of arrays of genotype probabilities, as calculated by `calc_genoprob()`.
`by`	Whether to summarize by individual or marker
`omit_x`	If TRUE, omit the X chromosome.
`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

The result is a vector of estimated heterozygosities

Examples

iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
p <- calc_genoprob(iron, err=0.002)

# heterozygosities by individual
het_ind <- calc_het(p)

# heterozygosities by marker
het_mar <- calc_het(p, "marker")

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