Fst-Heterozygosity Smoothed Quantiles

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Documentation for package ‘fsthet’ version 1.0.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

allele.counts	This counts the number of alleles at a locus.
bins	Example heterozygosity bins from fsthet.
calc.actual.fst	This calcualtes global Fsts from a genepop dataframe.
calc.allele.freq	This calculates allele frequencies.
calc.betahat	This calculates beta-hat, the Fst value used in Lositan.
calc.exp.het	This calculates expected heterozygosities.
calc.fst	This calculates Fst.
calc.theta	This calculates theta.
ci.means	This calculates the average confidence intervals from multiple bootstrap outputs.
cis	Example dataframe of smoothed quantiles from fsthet
cis.list	Example list of CI matrices from bootstrap output from numerical simulations
fhetboot	This is a wrapper to run the bootstrapping and plot the confidence intervals and significant loci.
find.outliers	This identifies all of the SNPs outside of the smoothed quantiles in the dataset.
find.quantiles	Generates quantiles from binned Fst values
fst.boot	This is the major bootstrapping function to calculate confidence intervals.
fst.boot.means	Calculates mean values within the bins.
fst.boot.onecol	This bootstraps across all individuals to calculate a bootstrapped Fst for a randomly-sampled locus.
fst.options.print	This prints the options for choosing an Fst calculation.
fsthet	This is a wrapper to generate and plot the smoothed quantiles and identify outliers.
fsts	Example fst calculations from a genepop file.
fsts.beta	Example fst calculations from a genepop file.
fsts.betahat	Example fst calculations from a genepop file.
fsts.theta	Example fst calculations from a genepop file.
gpop	Example genepop file from numerical simulations
make.bins	This sorts Fst values into a designated number of overlapping heterozygosity bins.
my.read.genepop	This reads a genepop file into R
p.boot	Calculates mean values within the bins.
plotting.cis	This plots a dataframe of fsts with bootstrapped confidence intervals.
quant.out	Example fsthet output based on numerical simulations
remove.spaces	This removes spaces from a character vector
var.fst	This calculates Cockerham & Weir's Beta.