Removes all but the specified loci from a genlight object

Source: R/gl.keep.loc.r

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).

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

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()

Author

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

Examples

# SNP data
  gl2 <- gl.keep.loc(testset.gl, loc.list=c('100051468|42-A/T', '100049816-51-A/G'))
#> Starting gl.keep.loc 
#>   Processing genlight object with SNP data
#>   List of loci to keep has been specified
#>   Warning: Listed loci 100051468|42-A/T not present in the dataset -- ignored
#>   Deleting all but the specified loci
#> Completed: gl.keep.loc 
#> 
# Tag P/A data
  gs2 <- gl.keep.loc(testset.gs, loc.list=c('20134188','19249144'))
#> Starting gl.keep.loc 
#>   Processing genlight object with Presence/Absence (SilicoDArT) data
#>   List of loci to keep has been specified
#>   Deleting all but the specified loci
#> Completed: gl.keep.loc 
#>