calc_het: Calculate heterozygosities

In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

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().

Details

calc_het() looks at the genotype names (the 2nd dimension of the dimnames of the input probs), which must be two-letter names, and assumes that when the two letters are different it's a heterozygous genotype while if they're the same it's a homozygous genotype

Value

The result is a vector of estimated heterozygosities

See Also

calc_raw_het(), calc_geno_freq()

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 May 29, 2024, 11:46 a.m.