dartR (version 0.80)

gl.recode.ind: Recode individual (=specimen) labels in a genelight or genind object {adegenet}

Description

This script recodes individual labels and/or deletes individuals from a DaRT genlight SNP file or a SilicoDArT genind file based on information provided in a csv file.

Usage

gl.recode.ind(gl, ind.recode)

Arguments

gl

-- name of the genlight object containing SNP genotypes or a genind object containing presence/absence data [required]

ind.recode

-- name of the csv file containing the individual relabelling [required]

Value

A genlight or genind object with the recoded and reduced data

Details

Renaming individuals may be required when there have been errors in labelling arising in the process from sample to DArT files. There may be occasions where renaming individuals is required for preparation of figures. Caution needs to be exercised because of the potential for breaking the "chain of evidence" between the samples themselves and the analyses. Recoding individuals can be done with a recode table (csv).

The script, having deleted individuals, identifies resultant monomorphic loci or loci with all values missing and deletes them (using gl.filter.monomorphs.r)

See Also

gl.filter.monomorphs

Examples

# NOT RUN {
   gl <- gl.recode.ind(testset.gl, ind.recode="testset_pop_recode.csv")
# }