Creates a proforma recode_pop_table file for reassigning population names

Renaming populations may be required when there have been errors in assignment arising in the process from sample to DArT 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 containing the SNP data [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]. Use outpath=getwd() or outpath='.' when calling this function to direct output files to your working directory.

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 vector containing the new population names.

Details

This script 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.

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

Author

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)
#> Starting gl.make.recode.pop 
#>   Processing genlight object with SNP data
#>   Writing draft lookup table to /tmp/RtmpWgoHDI/test.csv . Edit before use
#> Completed: gl.make.recode.pop 
#>