subset.calc_genoprob: Subsetting genotype probabilities

In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

Subsetting genotype probabilities

Description

Pull out a specified set of individuals and/or chromosomes from the results of calc_genoprob().

Usage

## S3 method for class 'calc_genoprob'
subset(x, ind = NULL, chr = NULL, ...)

## S3 method for class 'calc_genoprob'
x[ind = NULL, chr = NULL]

Arguments

x	Genotype probabilities as output from calc_genoprob().
ind	A vector of individuals: numeric indices, logical values, or character string IDs
chr	A vector of chromosomes: logical values, or character string IDs. Numbers are interpreted as character string IDs.
...	Ignored.

Value

An object of class "calc_genoprob", like the input, with the selected individuals and/or chromsomes; see calc_genoprob().

Examples

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

pr <- calc_genoprob(grav2)
# keep just individuals 1:5, chromosome 2
prsub <- pr[1:5,2]
# keep just chromosome 2
prsub2 <- pr[,2]

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