subset.phasedgeno: Subsetting phased genotype objects

In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

Subsetting phased genotype objects

Description

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

Usage

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

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

Arguments

x	Imputed genotypes as output from guess_phase(), a list of 3d arrays.
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 "phasedgeno", like the input, with the selected individuals and/or chromosomes; see guess_phase().

See Also

guess_phase(), cbind.phasedgeno(), rbind.phasedgeno()

Examples

## Not run: 
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/main/DOex/DOex.zip")
DOex <- read_cross2(file)
pr <- calc_genoprob(DOex, error_prob=0.002)
m <- maxmarg(pr)
ph <- guess_phase(DOex, m)
ph <- ph[1:10,] # first ten individuals
ph <- ph[,2]  # chromosome 2

## End(Not run)

qtl2 documentation built on July 6, 2026, 5:11 p.m.