GELATo - Group ExcLusion and Assignment Test

Share:

Description

Run a GELATo test to evaluate assignment likelihoods of groups of samples.

Usage

1
2
3
gelato(g, unknown.strata, nrep = 1000, min.sample.size = 5)

gelatoPlot(gelato.result, unknown, main = NULL)

Arguments

g

a gtypes object.

unknown.strata

a character vector listing to assign. Strata must occur in g.

nrep

number of permutation replicates for Fst distribution.

min.sample.size

minimum number of samples to use to characterize knowns. If the known sample size would be smaller than this after drawing an equivalent number of unknowns for self-assignment, then the comparison is not done.

gelato.result

the result of a call to gelato.

unknown

the name of an unknown stratum in the x$likelihoods element.

main

main label for top of plot.

Value

A list with the following elements:

assign.prob a data.frame of assignment probabilities.
likelihoods a list of likelihoods.

Author(s)

Eric Archer eric.archer@noaa.gov

References

O'Corry-Crowe, G., W. Lucey, F.I. Archer, and B. Mahoney. 2015. The genetic ecology and population origins of the beluga whales of Yakutat Bay. Marine Fisheries Review.

Examples

1
2
3
4
5
6
7
8
data(msats.g)

# Run GELATo analysis
gelato.fine <- gelato(msats.g, unk = "Offshore.South", nrep = 10)
gelato.fine

# Plot results
gelatoPlot(gelato.fine, "Offshore.South")

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.