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Removes all but the specified individuals from a genlight {adegenet} object

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.

Usage

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

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].

Value

A genlight object with the reduced data

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 
#>