gl.assign.grm: Population assignment using grm

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Population assignment using grm

Description

This function takes one individual and estimates their probability of coming from individual populations from multilocus genotype frequencies.

Usage

gl.assign.grm(x, unknown, verbose = NULL)

Arguments

x	Name of the genlight object containing the SNP data [required].
unknown	Name of the individual to be assigned to a 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, unless specified using gl.set.verbosity].

Details

This function is a re-implementation of the function multilocus_assignment from package gstudio. Description of the method used in this function can be found at: https://dyerlab.github.io/applied_population_genetics/population-assignment.html

Value

A data.frame consisting of assignment probabilities for each population.

Author(s)

Custodian: Luis Mijangos – Post to https://groups.google.com/d/forum/dartr

Examples

require("dartR.data")
if ((requireNamespace("rrBLUP", quietly = TRUE)) &(requireNamespace("gplots", quietly = TRUE)) ) {
res <- gl.assign.grm(platypus.gl,unknown="T27")
}

dartR documentation built on June 8, 2023, 6:48 a.m.