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gl.drop.loc

Remove specified loci from a genelight {adegenet} object

Description

The script returns a genlight object with specified loci deleted.

Usage

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

Arguments

x

– name of the genlight object containing SNP genotypes or presence/absence data [required]
loc.list

– a list of loci to be deleted [required, if loc.range not specified]
first

– first of a range of loci to be deleted [required, if loc.list not specified]
last

– last of a range of loci to be deleted [if not specified, last locus in the dataset]
verbose

– verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 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)

Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

Examples

# SNP data
  gl2 <- gl.drop.loc(testset.gl, loc.list=c("100051468|42-A/T", "100049816-51-A/G"))
# Tag P/A data
  gs2 <- gl.drop.loc(testset.gs, loc.list=c("20134188","19249144"))
dartR

Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis

v1.9.6
GPL-2
Authors
Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb]
Initial release
2021-04-29

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