fsthet (version 1.0.1)

fhetboot: This is a wrapper to run the bootstrapping and plot the confidence intervals and significant loci.

Description

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

Usage

fhetboot(gpop, fst.choice="fst", alpha=0.05,nreps=10)

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 confidence intervals and the p-value adjustment calculations (default is 0.05).

nreps

The number of bootstrap replicates to use. The default is 10.

Value

fsts

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

Examples

# NOT RUN {
  
# }
# NOT RUN {
  
# }
# NOT RUN {
    gfile<-system.file("extdata", "example.genepop.txt",package = 'fsthet')
    gpop<-my.read.genepop(gfile)
    out.dat<-fhetboot(gpop, fst.choice="fst", alpha=0.05,nreps=10)
  
# }