Merges two or more populations in a genlight object into one population

Individuals are assigned to populations based on the specimen metadata data file (csv) used with gl.read.dart().

This script assigns individuals from two nominated populations into a new single population. It can also be used to rename populations.

The script returns a genlight object with the new population assignments.

Usage

gl.merge.pop(x, old = NULL, new = NULL, verbose = NULL)

Arguments

x

Name of the genlight object containing SNP genotypes [required].

old

A list of populations to be merged [required].

new

Name of the new population [required].

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 genlight object with the new population assignments.

Author

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

Examples

   gl <- gl.merge.pop(testset.gl, old=c('EmsubRopeMata','EmvicVictJasp'), new='Outgroup')
#> Starting gl.merge.pop 
#>   Processing genlight object with SNP data
#>   Merging a list of populations into one
#>   Merging EmsubRopeMata EmvicVictJasp into Outgroup 
#> Completed: gl.merge.pop 
#>