gl.keep.pop: Removes all but the specified populations from a genlight...

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

Removes all but the specified populations from a genlight object

Description

Individuals are assigned to populations based on the specimen metadata data file (csv) used with gl.read.dart().

The script, having deleted the specified populations, 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 new population assignments and 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.pop(
  x,
  pop.list,
  as.pop = NULL,
  recalc = FALSE,
  mono.rm = FALSE,
  verbose = NULL
)

Arguments

x	Name of the genlight object containing the SNP or presence/absence (SilicoDArT) data [required].
pop.list	A list of populations to be kept [required].
as.pop	Assign another metric to represent population [default NULL].
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.pop to drop rather than keep specified populations

Examples

 # SNP data
   gl2 <- gl.keep.pop(testset.gl, pop.list=c('EmsubRopeMata', 'EmvicVictJasp'))
   gl2 <- gl.keep.pop(testset.gl, pop.list=c('EmsubRopeMata', 'EmvicVictJasp'),
   mono.rm=TRUE,recalc=TRUE)
   gl2 <- gl.keep.pop(testset.gl, pop.list=c('Female'),as.pop='sex')
 # Tag P/A data
   gs2 <- gl.keep.pop(testset.gs, pop.list=c('EmsubRopeMata','EmvicVictJasp'))

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.