gl.drop.pop: Removes specified populations from a genlight object

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

Removes specified populations from a genlight object

Description

Individuals are assigned to populations based on the specimen metadata file (csv) used with gl.read.dart. The script, having deleted 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.drop.pop(
  x,
  pop.list,
  as.pop = NULL,
  recalc = FALSE,
  mono.rm = FALSE,
  verbose = NULL
)

Arguments

x	Name of the genlight object containing SNP genotypes or Tag P/A data (SilicoDArT) [required].
pop.list	A list of populations to be removed [required].
as.pop	Temporarily assign another metric to represent population for the purposes of deletions [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.keep.pop to keep rather than drop specified populations

Examples

 # SNP data
   gl2 <- gl.drop.pop(testset.gl,
   pop.list=c('EmsubRopeMata','EmvicVictJasp'),verbose=3)
   gl2 <- gl.drop.pop(testset.gl, pop.list=c('EmsubRopeMata','EmvicVictJasp'),
   mono.rm=TRUE,recalc=TRUE)
   gl2 <- gl.drop.pop(testset.gl, pop.list=c('Male','Unknown'),as.pop='sex',verbose=3)
 # Tag P/A data
   gs2 <- gl.drop.pop(testset.gs, pop.list=c('EmsubRopeMata','EmvicVictJasp'))

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