fhetboot function

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

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.

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.

Returns

• 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:

    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)
## End(Not run)