| gl.reassign.pop {dartR} | R Documentation |
Assigns an individual metric as pop in a genlight {adegenet} object
Description
Individuals are assigned to populations based on the individual/sample/specimen metrics file (csv) used with gl.read.dart().
One might want to define the population structure in accordance with another classification, such as using an individual metric (e.g. sex, male or female). This script discards the current population assignments and replaces them with new population assignments defined by a specified individual metric.
The script returns a genlight object with the new population assignments. Note that the original population assignments are lost.
Usage
gl.reassign.pop(x, as.pop, verbose = NULL)
Arguments
x |
Name of the genlight object containing SNP genotypes [required]. |
as.pop |
Specify the name of the individual metric to set as the pop variable [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 reassigned populations.
Author(s)
Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr
Examples
# SNP data
popNames(testset.gl)
gl <- gl.reassign.pop(testset.gl, as.pop='sex',verbose=3)
popNames(gl)
# Tag P/A data
popNames(testset.gs)
gs <- gl.reassign.pop(testset.gs, as.pop='sex',verbose=3)
popNames(gs)