fsthet (version 1.0.1)

fsthet: This is a wrapper to generate and plot the smoothed quantiles and identify outliers.

Description

This calcualtes global Fsts from a genepop dataframe and then does: calculates smoothed quantiles plots the Heterozygosity-Fst relationship with smoothed quantiles outputs the loci lying outside the quantiles. Returns a data frame containing Locus ID, Ht, Fst, and a true/false value of whether it's an outlier.

Usage

fsthet(gpop, fst.choice="fst", alpha=0.05)

Arguments

gpop

Provide the genepop dataframe (from my.read.genepop).

fst.choice

Specify which type of fst calculation should be used. See fst.options.print for the choices.

alpha

The alpha value for the quantiles (default is 0.05 to generate 95 percent quantiles).

Value

fsts

This returns a dataframe with Locus, Ht, Fst, and True/False of whether it's an outlier.

Examples

# NOT RUN {
  
# }
# NOT RUN {
  gfile<-system.file("extdata", "example.genepop.txt",package = 'fsthet')
  gpop<-my.read.gpop(gfile)
  out.dat<-fsthet(gpop)
# }