gl.keep.loc: Removes all but the specified loci from a genlight object

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Removes all but the specified loci from a genlight object

Description

This function deletes loci that are not specified to keep, and their associated metadata.

The script returns a dartR genlight object with the retained loci. The script works with both genlight objects containing SNP genotypes and Tag P/A data (SilicoDArT).

Usage

gl.keep.loc(x, loc.list = NULL, first = NULL, last = NULL, verbose = NULL)

Arguments

x	Name of the genlight object [required].
loc.list	A list of loci to be kept [required, if loc.range not specified].
first	First of a range of loci to be kept [required, if loc.list not specified].
last	Last of a range of loci to be kept [if not specified, last locus in the dataset].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress but not results; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].

Value

A genlight object with the reduced data

Author(s)

Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr

See Also

gl.drop.loc to drop rather than keep specified loci

Other dartR-base: gl.drop.ind(), gl.drop.loc(), gl.drop.pop(), gl.edit.recode.ind(), gl.edit.recode.pop(), gl.make.recode.ind(), gl.read.dart(), gl.recode.ind(), gl.recode.pop(), gl.set.verbosity()

Examples

# SNP data
  gl2 <- gl.keep.loc(testset.gl, loc.list=c('100051468|42-A/T', '100049816-51-A/G'))
# Tag P/A data
  gs2 <- gl.keep.loc(testset.gs, loc.list=c('20134188','19249144'))

dartR documentation built on April 4, 2025, 12:23 a.m.