calc_geno_freq: Calculate genotype frequencies

In rqtl/qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

Calculate genotype frequencies

Description

Calculate genotype frequencies, by individual or by marker

Usage

calc_geno_freq(probs, by = c("individual", "marker"), omit_x = TRUE)

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, results are just for the autosomes. If FALSE, results are a list of length two, containing the results for the autosomes and those for the X chromosome.

Value

If omit_x=TRUE, the result is a matrix of genotype frequencies; columns are genotypes and rows are either individuals or markers.

If necessary (that is, if omit_x=FALSE, the data include the X chromosome, and the set of genotypes on the X chromosome are different than on the autosomes), the result is a list with two components (for the autosomes and for the X chromosome), each being a matrix of genotype frequencies.

See Also

calc_raw_geno_freq(), calc_het()

Examples

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

# genotype frequencies by marker
tab_g <- calc_geno_freq(p, "marker")

# allele frequencies by marker
ap <- genoprob_to_alleleprob(p)
tab_a <- calc_geno_freq(ap, "marker")

rqtl/qtl2 documentation built on March 20, 2024, 6:35 p.m.