gl.make.recode.pop: Creates a proforma recode_pop_table file for reassigning...

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

Creates a proforma recode_pop_table file for reassigning population names

Description

Renaming populations may be required when there have been errors in assignment arising in the process from sample to sequence files or when one wishes to amalgamate populations, or delete populations. Recoding populations can also be done with a recode table (csv).

Usage

gl.make.recode.pop(
  x,
  out.recode.file = "recode_pop_table.csv",
  outpath = tempdir(),
  verbose = NULL
)

Arguments

x	Name of the genlight object [required].
out.recode.file	File name of the output file (including extension) [default recode_pop_table.csv].
outpath	Path where to save the output file [default tempdir(), mandated by CRAN].
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

This function facilitates the construction of a recode table by producing a proforma file with current population names in two identical columns. Edit the second column to reassign populations. Use keyword 'Delete' to delete a population.

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 clear record of the changes.

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

The function works with both genlight objects containing SNP genotypes and Tag P/A data (SilicoDArT).

Apply the recoding using gl.recode.pop().

Value

A vector containing the new population names.

Author(s)

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

Examples

result <- gl.make.recode.pop(testset.gl,out.recode.file='test.csv',outpath=tempdir(),verbose=2)

dartR documentation built on April 4, 2025, 12:23 a.m.