getAllele: Obtain reference allele information of markers

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

Obtain reference allele information of markers

Description

This function returns the reference allele and alternative allele(s).

Usage

getAllele(object, valid = TRUE, chr = NULL, ...)

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

Arguments

object	A GbsrGenotypeData object.
valid	A logical value. See details.
chr	A index to spefcify chromosome to get information.
...	Unused.

Details

If valid = TRUE, the alleles of 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 strings each of which is a "/" separated string and indicates the reference allele and the alternative allele(s) at a marker.

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)

getAllele(gds)

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

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