getChromosome: Obtain chromosome IDs of markers

In tomoyukif/GBScleanR: Error correction tool for noisy genotyping by sequencing (GBS) data

Obtain chromosome IDs of markers

Description

This function returns chromosome IDs of markers.

Usage

getChromosome(object, valid = TRUE, ...)

## S4 method for signature 'GbsrGenotypeData'
getChromosome(object, valid)

Arguments

object	A GbsrGenotypeData object.
valid	A logical value. See details.
...	Unused.

Details

If valid = TRUE, the chromosome IDs of the markers which are labeled TRUE in the "valid" column of the "marker" slot will be returned. If you need the number of over all markers, set valid = FALSE. validMar() tells you which markers are valid.

Value

A vector of factors indicating chromosome IDs.

Examples

# Load data in the GDS file and instantiate a [GbsrGenotypeData] object.
gds_fn <- system.file("extdata", "sample.gds", package = "GBScleanR")
gds <- loadGDS(gds_fn)

getChromosome(gds)

# Close the connection to the GDS file.
closeGDS(gds)

tomoyukif/GBScleanR documentation built on Oct. 31, 2024, 2:43 a.m.