gl.edit.recode.pop: Creates or edits a population re-assignment table

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

Creates or edits a population re-assignment table

Description

A script to edit population assignments in a genlight object, or to create a reassignment table taking the population assignments from a genlight object, or to edit existing population assignments in a pop.recode.table.

Usage

gl.edit.recode.pop(
  x,
  pop.recode = NULL,
  out.recode.file = NULL,
  outpath = tempdir(),
  recalc = FALSE,
  mono.rm = FALSE,
  verbose = NULL
)

Arguments

x	Name of the genlight object for which populations are to be reassigned [required].
pop.recode	Path to recode file [default NULL].
out.recode.file	Name of the file to output the new individual labels [default NULL].
outpath	Path where to save the output file [default tempdir(), mandated by CRAN].
recalc	Recalculate the locus metadata statistics if any individuals are deleted [default TRUE].
mono.rm	Remove monomorphic loci [default TRUE].
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

Genlight objects assign specimens to populations based on information in the ind.metadata file provided when the genlight object is first generated. Often one wishes to subset the data by deleting populations or to amalgamate populations. This can be done with a pop.recode table with two columns. The first column is the population assignment in the genlight object, the second column provides the new assignment.

This script will input an existing reassignment table for editing and optionally save it as a new table, or if the name of an input table is not supplied, will generate a table using the population assignments in the parent genlight object.

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.

Use outpath=getwd() or outpath='.' when calling this function to direct output files to your working directory.

The script returns a genlight object with the new population assignments and the recalculated locus metadata.

Value

An object of class ('genlight') with the revised population assignments

Author(s)

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

See Also

gl.recode.pop, gl.drop.pop, gl.keep.pop, gl.merge.pop, gl.reassign.pop

Examples

## Not run: 
gl <- gl.edit.recode.pop(testset.gl)
gs <- gl.edit.recode.pop(testset.gs)

## End(Not run)

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