qtl2: compare_geno – R documentation

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compare_geno

Compare individuals' genotype data

Description

Count the number of matching genotypes between all pairs of individuals, to look for unusually closely related individuals.

Usage

compare_geno(cross, omit_x = FALSE, proportion = TRUE, quiet = TRUE, cores = 1)

Arguments

`cross`	Object of class `"cross2"`. For details, see the R/qtl2 developer guide.
`omit_x`	If TRUE, only use autosomal genotypes
`proportion`	If TRUE (the default), the upper triangle of the result contains the proportions of matching genotypes. If FALSE, the upper triangle contains counts of matching genotypes.
`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 square matrix; diagonal is number of observed genotypes for each individual. The values in the lower triangle are the numbers of markers where both of a pair were genotyped. The values in the upper triangle are either proportions or counts of matching genotypes for each pair (depending on whether proportion=TRUE or =FALSE). The object is given class "compare_geno".

Examples

grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2"))
cg <- compare_geno(grav2)
summary(cg)

qtl2

Quantitative Trait Locus Mapping in Experimental Crosses

v0.24

GPL-3

Authors

Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>), R Core Team [ctb]

Initial release

2020-12-16