gl.recode.pop {dartR.base}

Recodes population assignments in a genlight object

Description

This function recodes population assignments and/or deletes populations from a DaRT genlight object based on information provided in a csv population recode file.

Usage

gl.recode.pop(x, pop.recode, recalc = FALSE, mono.rm = FALSE, verbose = NULL)

Arguments

x

Name of the genlight object [required].

pop.recode

Name of the csv file containing the population reassignments [required].

recalc

If TRUE, recalculates the locus metadata statistics if any individuals are deleted in the filtering [default FALSE].

mono.rm

If TRUE, removes 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

Individuals are assigned to populations based on the specimen metadata data file (csv) used with gl.read.dart(). Recoding can be used to amalgamate populations or to selectively delete or retain populations. When caution needs to be exercised because of the potential for breaking the 'chain of evidence' associated with the samples, recoding individuals using a recode table (csv) can provide a durable record of the changes. The population recode file contains a list of populations taken from the genlight object as the first column of the csv file, and the new population assignments are located in the second column of the csv file. The keyword 'Delete' used as a new population assignment will result in the associated specimen being dropped from the dataset. The function works with genlight objects containing SNP genotypes and Tag P/A data (SilicoDArT). For SNP genotype data, the function, having deleted populations, optionally identifies resultant monomorphic loci or loci with all values missing and deletes them. The script also optionally recalculates the locus metadata as appropriate. The optional deletion of monomorphic loci and the optional recalculation of locus statistics is not available for Tag P/A data (SilicoDArT).

Value

A genlight object with the recoded and reduced data.

Author(s)

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

See Also

gl.filter.monomorphs

gl.recode.pop

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.keep.pop(), gl.make.recode.ind(), gl.merge.pop(), gl.reassign.pop(), gl.recode.ind(), gl.rename.pop(), gl.sample(), gl.sim.genotypes(), gl.sort(), gl.subsample.ind(), gl.subsample.loc()

Examples

  mfile <- system.file('extdata', 'testset_pop_recode.csv', package='dartR.data')
  nPop(testset.gl)
  gl <- gl.recode.pop(testset.gl, pop.recode=mfile, verbose=3)