dartR (version 1.1.11)

gl.report.pa: Report number of private alleles possessed by an individual of unknown provenance

Description

This script calculates the number of private alleles possessed by a focal individual of unknown provenance when compared to a series of target populations.

Usage

gl.report.pa(x, id, nmin = 10, threshold = 0, v = 2)

Arguments

x

-- name of the input genlight object [required]

id

-- identity label 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

-- retain those populations for which the focal individual has private alleles less or equal in number than the threshold [default 0]

v

-- verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2]

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 thresold t.

Details

A private allele is an allele possessed by the focal individual, but absent from the target population. It differs from a fixed allelic difference in that the focal individual may be heterozygous, in which case can share one but not both of its alleles with the target population.

Examples

# NOT RUN {
# Test run with a focal individual from the Macleay River (EmmacMaclGeor)
x <- gl.report.pa(testset.gl, id="UC_00146", nmin=10, threshold=1, v=3)

# }