Population assignment using grm

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

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].

Value

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

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

Author

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")
}
#> Registered S3 method overwritten by 'gplots':
#>   method         from 
#>   reorder.factor gdata
#> Starting gl.assign.grm 
#>   Processing genlight object with SNP data
#>   Warning: data include loci that are scored NA across all individuals.
#>   Consider filtering using gl <- gl.filter.allna(gl)
#>