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

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.

See also

gl.assign.pca

Author

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

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)
#> Starting gl.assign.pa 
#>   Processing genlight object with SNP data
#>   Discarding 10 populations with sample size < 10 :
#> EmmacClarJack, EmmacClarYate, EmmacMDBGwyd, EmmacMaryBoru, EmmacMaryPetr, EmmacNormJack, EmmacNormLeic, EmmacNormSalt, EmsubRopeMata, EmvicVictJasp 
#>   Assigning 1 unknown individual UC_00146 to 20 target populations using 215 loci
#>   Table showing populations against number of loci with private 
#>             alleles
#>    0 EmmacMaclGeor 
#>    1 EmmacBurnBara EmmacRichCasi EmmacTweeUki 
#>   >1 ---   2 EmmacBrisWive EmmacMDBBowm EmmacMDBCudg EmmacMDBForb EmmacMDBMaci EmmacMDBMurrMung 
#>   >1 ---   3 EmmacFitzAllig EmmacMDBCond EmmacMDBSanf EmmacRussEube 
#>   >1 ---   4 EmmacBurdMist EmmacJohnWari EmmacRoss 
#>   >1 ---   6 EmmacCoopEulb 
#>   >1 ---   7 EmmacCoopCully 
#>   >1 ---   16 EmmacCoopAvin 
#>   Identified and retained 4 putative source populations for UC_00146  (the unknown) based on the specified threshold
#>   Monomorphic loci removed
#> Completed: gl.assign.pa 
#>