gl.keep.ind: Removes all but the specified individuals from a genlight...

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Removes all but the specified individuals from a genlight object

Description

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).

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

Author(s)

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

See Also

gl.drop.ind to drop rather than keep specified individuals

Examples

  # SNP data
    gl2 <- gl.keep.ind(testset.gl, ind.list=c('AA019073','AA004859'))
  # Tag P/A data
   gs2 <- gl.keep.ind(testset.gs, ind.list=c('AA020656','AA19077','AA004859'))

dartR documentation built on June 8, 2023, 6:48 a.m.