gl.outflank: Identifies loci under selection per population using the...

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

Identifies loci under selection per population using the outflank method of Whitlock and Lotterhos (2015)

Description

Identifies loci under selection per population using the outflank method of Whitlock and Lotterhos (2015)

Usage

gl.outflank(
  gi,
  plot = TRUE,
  LeftTrimFraction = 0.05,
  RightTrimFraction = 0.05,
  Hmin = 0.1,
  qthreshold = 0.05,
  ...
)

Arguments

gi	A genlight or genind object, with a defined population structure [required].
plot	A switch if a barplot is wanted [default TRUE].
LeftTrimFraction	The proportion of loci that are trimmed from the lower end of the range of Fst before the likelihood function is applied [default 0.05].
RightTrimFraction	The proportion of loci that are trimmed from the upper end of the range of Fst before the likelihood function is applied [default 0.05].
Hmin	The minimum heterozygosity required before including calculations from a locus [default 0.1].
qthreshold	The desired false discovery rate threshold for calculating q-values [default 0.05].
...	additional parameters (see documentation of outflank on github).

Details

This function is a wrapper around the outflank function provided by Whitlock and Lotterhos. To be able to run this function the packages qvalue (from bioconductor) and outflank (from github) needs to be installed. To do so see example below.

Value

Returns an index of outliers and the full outflank list

References

Whitlock, M.C. and Lotterhos K.J. (2015) Reliable detection of loci responsible for local adaptation: inference of a neutral model through trimming the distribution of Fst. The American Naturalist 186: 24 - 36.

Github repository: Whitlock & Lotterhos: https://github.com/whitlock/OutFLANK (Check the readme.pdf within the repository for an explanation. Be aware you now can run OufFLANK from a genlight object)

See Also

utils.outflank, utils.outflank.plotter, utils.outflank.MakeDiploidFSTMat

Examples

gl.outflank(bandicoot.gl, plot = TRUE)

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