Removes all but the specified individuals from a dartR genlight object

Source: R/gl.keep.ind.r

This script deletes all individuals apart from those listed (ind.list). Monomorphic loci and loci that are scored all NA are optionally deleted (mono.rm=TRUE). The script also optionally recalculates locus metatdata statistics to accommodate the deletion of individuals from the dataset (recalc=TRUE).

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

gl.keep.ind(x, ind.list, recalc = FALSE, mono.rm = FALSE, verbose = NULL)

Arguments

x

Name of the genlight object [required].

ind.list

A list of individuals to be retained [required].

recalc

If TRUE, recalculate the locus metadata statistics [default FALSE].

mono.rm

If TRUE, remove monomorphic and all NA 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].

Value

A reduced dartR genlight object

See also

gl.drop.pop to drop rather than keep specified populations

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 
#>