subset_feather_genoprob: Subsetting genotype probabilities

In byandell/qtl2feather: Feather Database for R/qtl2 Genotype Probabilities

Description

Pull out a specified set of individuals and/or chromosomes from the results of feather_genoprob.

Usage

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

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

Arguments

x	Genotype probabilities as output from feather_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 <- feather_genoprob(pr, "grav2", dir)
# keep just individuals 1:5, chromosome 2
prsub <- fpr[1:5,2]
# keep just chromosome 2
prsub2 <- fpr[,2]

byandell/qtl2feather documentation built on May 13, 2019, 9:30 a.m.