subset_fst_genoprob: Subsetting genotype probabilities

In kbroman/qtl2fst: Database Storage of Genotype Probabilities for QTL Mapping

Subsetting genotype probabilities

Description

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

Usage

subset_fst_genoprob(x, ind = NULL, chr = NULL, mar = NULL, ...)

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

Arguments

x	Genotype probabilities as output from fst_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.
mar	A vector of marker names as character string IDs.
...	Ignored.

Value

The input genotype probabilities, with the selected individuals and/or chromsomes.

Examples

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

pr <- calc_genoprob(grav2)
dir <- tempdir()
fpr <- fst_genoprob(pr, "grav2", dir)

# keep just individuals 1:5, chromosome 2
prsub <- fpr[1:5,2]
# keep just chromosome 2
prsub2 <- fpr[,2]

# clean up: remove all the files we created
unlink(fst_files(fpr))

kbroman/qtl2fst documentation built on May 3, 2023, 11:12 a.m.