gl.assign.pa: Eliminates populations as possible source populations for an...

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

Eliminates populations as possible source populations for an individual of unknown provenance, using private alleles

Description

This script eliminates from consideration as putative source populations, those populations for which the individual has too many private alleles. The populations that remain are putative source populations, subject to further consideration.

The algorithm identifies those target populations for which the individual has no private alleles or for which the number of private alleles does not exceed a user specified threshold.

An excessive count of private alleles is an indication that the unknown does not belong to a target population (provided that the sample size is adequate, say >=10).

Usage

gl.assign.pa(
  x,
  unknown,
  nmin = 10,
  threshold = 0,
  n.best = NULL,
  verbose = NULL
)

Arguments

x	Name of the input genlight object [required].
unknown	SpecimenID label (indName) of the focal individual whose provenance is unknown [required].
nmin	Minimum sample size for a target population to be included in the analysis [default 10].
threshold	Populations to retain for consideration; those for which the focal individual has less than or equal to threshold loci with private alleles [default 0].
n.best	If given a value, dictates the best n=n.best populations to retain for consideration (or more if their are ties) based on private alleles [default NULL].
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 containing the focal individual (assigned to population 'unknown') and populations for which the focal individual is not distinctive (number of loci with private alleles less than or equal to the threshold). If no such populations, the genlight object contains only data for the unknown individual.

Author(s)

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

See Also

gl.assign.pca

Examples

# Test run with a focal individual from the Macleay River (EmmacMaclGeor)
  test <- gl.assign.pa(testset.gl, unknown='UC_00146', nmin=10, threshold=1,
  verbose=3)

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.