dartR (version 0.80)

gi.outflank: Functio to identify loci under selection per population using the outflank method of Whitlock and Lotterhos (2015)

Description

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

Usage

gi.outflank(gi, plot = TRUE)

Arguments

gi

a genind object, with a defined population structure

plot

a switch if a barplot is wanted.

Value

returns an index of outliers and the full outflank list

Details

this function is a wrapper around the outflank function provided by Whitlock and Lotterhus. 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.

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.

Examples

# NOT RUN {
#install qvalue from bioconductor and outflank from github 
source("http://bioconductor.org/biocLite.R")
biocLite("qvalue") 
library(devtools)
install_github("Whitlock/OutFLANK")
# now we are able to run outflank using a genlight object
gi.outflank(gi, plot = TRUE)
# }