gl.edit.recode.ind {dartR.base}

Creates or edits individual (=specimen) names, creates a recode_ind file and applies the changes to a genlight object @family data manipulation

Description

A function to edit names of individual in a dartR genlight object, or to create a reassignment table taking the individual labels from a genlight object, or to edit existing individual labels in an existing recode_ind file. The amended recode table is then applied to the genlight object.

Usage

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

Arguments

x

Name of the genlight object [required].

out.recode.file

Name of the file to output the new individual labels [optional].

outpath

Directory to save the plot RDS files [default as specified by the global working directory or tempdir()]

recalc

If TRUE, recalculate the locus metadata statistics [default TRUE].

mono.rm

If TRUE, remove monomorphic loci [default TRUE].

verbose

Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress but not results; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].

Details

Renaming individuals may be required when there have been errors in labeling arising in the passage of samples to sequencing. There may be occasions where renaming individuals is required for preparation of figures. This function will input an existing recode 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 individual labels in the parent genlight object. 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. For SNP genotype data, the function, having deleted individuals, 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). Use outpath=getwd() when calling this function to direct output files to your working directory. The function returns a dartR genlight object with the new population assignments and the recalculated locus metadata.

Value

An object of class ('genlight') with the revised individual labels.

Author(s)

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

See Also

gl.recode.ind, gl.drop.ind, gl.keep.ind

Examples

#this is an interactive example
if(interactive()){
gl <- gl.edit.recode.ind(testset.gl)
gl <- gl.edit.recode.ind(testset.gl, out.recode.file='ind.recode.table.csv')
}