Removes all but the specified individuals from a genlight object
Source:R/gl.keep.ind.r
gl.keep.ind.Rd
The script, having deleted individuals, optionally identifies resultant monomorphic loci or loci with all values missing and deletes them (using gl.filter.monomorphs.r). The script also optionally recalculates statistics made redundant by the deletion of individuals from the dataset.
The script returns a genlight object with the individuals deleted and, optionally, the recalculated locus metadata.
See more about data manipulation in the [tutorial](http://georges.biomatix.org/storage/app/media/uploaded-files/tutorial4dartrdatamanipulation22-dec-21-3.pdf).
Arguments
- x
Name of the genlight object containing the SNP or presence/absence (SilicoDArT) data [required].
- ind.list
A list of individuals to be removed [required].
- recalc
Recalculate the locus metadata statistics [default FALSE].
- mono.rm
Remove monomorphic loci [default FALSE].
- 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].
See also
gl.drop.ind
to drop rather than keep specified
individuals
Author
Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr
Examples
# SNP data
gl2 <- gl.keep.ind(testset.gl, ind.list=c('AA019073','AA004859'))
#> Starting gl.keep.ind
#> Processing genlight object with SNP data
#> Deleting all but the listed individuals AA019073, AA004859
#> Warning: Resultant dataset may contain monomorphic loci
#> Locus metrics not recalculated
#> Completed: gl.keep.ind
#>
# Tag P/A data
gs2 <- gl.keep.ind(testset.gs, ind.list=c('AA020656','AA19077','AA004859'))
#> Starting gl.keep.ind
#> Processing genlight object with Presence/Absence (SilicoDArT) data
#> Warning: Listed individual AA004859 not present in the dataset -- ignored
#> Deleting all but the listed individuals AA020656, AA19077
#> Warning: Resultant dataset may contain monomorphic loci
#> Locus metrics not recalculated
#> Completed: gl.keep.ind
#>