getSamID: Obtain the sample IDs

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

Obtain the sample IDs

Description

This function returns sample IDs.

Usage

getSamID(object, valid = TRUE, parents = FALSE, ...)

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

Arguments

object	A GbsrGenotypeData object.
valid	A logical value. See details.
parents	A logical value whether to include data for parents or not.
...	Unused.

Details

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

Value

A character vector of sample 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)

getSamID(gds)

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

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