dartR: gl.drop.pop – R documentation

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gl.drop.pop

Remove specified populations from a genelight {adegenet} object

Description

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

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]

Details

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.

Value

A genlight object with the reduced data

Author(s)

Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

Examples

# SNP data
   gl2 <- gl.drop.pop(testset.gl, pop.list=c("EmsubRopeMata","EmvicVictJasp"))
   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")
 # Tag P/A data  
   gs2 <- gl.drop.pop(testset.gs, pop.list=c("EmsubRopeMata","EmvicVictJasp"))

dartR

Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis

v1.9.6

GPL-2

Authors

Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb]

Initial release

2021-04-29