gl.keep.pop {dartR.base}

Removes all but the specified populations from a dartR genlight object

Description

Individuals are assigned to populations based on associated specimen metadata stored in the dartR genlight object. This script deletes all individuals apart from those in listed populations (pop.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 populations and the recalculated locus metadata. The script works with both genlight objects containing SNP genotypes and Tag P/A data (SilicoDArT).

Usage

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

Arguments

x

Name of the genlight object [required].

pop.list

List of populations to be retained [required].

as.pop

Temporarily assign another locus metric as the population for the purposes of deletions [default NULL].

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 but not results; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].

Value

A reduced dartR genlight object

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

Other data manipulation: gl.define.pop(), gl.drop.ind(), gl.drop.loc(), gl.drop.pop(), gl.edit.recode.pop(), gl.impute(), gl.join(), gl.keep.ind(), gl.keep.loc(), gl.make.recode.ind(), gl.merge.pop(), gl.reassign.pop(), gl.recode.ind(), gl.recode.pop(), gl.rename.pop(), gl.sample(), gl.sim.genotypes(), gl.sort(), gl.subsample.ind(), gl.subsample.loc()

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'))