Learn R Programming

fsthet (version 1.0.1)

Fst-Heterozygosity Smoothed Quantiles

Description

A program to generate smoothed quantiles for the Fst-heterozygosity distribution. Designed for use with large numbers of loci (e.g., genome-wide SNPs). The best case for analyzing the Fst-heterozygosity distribution is when many populations (>10) have been sampled. See Flanagan & Jones (2017) .

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Version

Install

install.packages('fsthet')

Monthly Downloads

193

Version

1.0.1

License

GPL-2

Maintainer

Sarah Flanagan

Last Published

March 20th, 2018

Functions in fsthet (1.0.1)

bins

Example heterozygosity bins from fsthet.
calc.theta

This calculates theta.
cis

Example dataframe of smoothed quantiles from fsthet
ci.means

This calculates the average confidence intervals from multiple bootstrap outputs.
calc.exp.het

This calculates expected heterozygosities.
allele.counts

This counts the number of alleles at a locus.
calc.allele.freq

This calculates allele frequencies.
fsthet

This is a wrapper to generate and plot the smoothed quantiles and identify outliers.
calc.actual.fst

This calcualtes global Fsts from a genepop dataframe.
fsts

Example fst calculations from a genepop file.
fst.boot.onecol

This bootstraps across all individuals to calculate a bootstrapped Fst for a randomly-sampled locus.
quant.out

Example fsthet output based on numerical simulations
cis.list

Example list of CI matrices from bootstrap output from numerical simulations
remove.spaces

This removes spaces from a character vector
fst.options.print

This prints the options for choosing an Fst calculation.
fst.boot

This is the major bootstrapping function to calculate confidence intervals.
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.
fst.boot.means

Calculates mean values within the bins.
find.quantiles

Generates quantiles from binned Fst values
fsts.theta

Example fst calculations from a genepop file.
make.bins

This sorts Fst values into a designated number of overlapping heterozygosity bins.
p.boot

Calculates mean values within the bins.
fsts.beta

Example fst calculations from a genepop file.
gpop

Example genepop file from numerical simulations
fsts.betahat

Example fst calculations from a genepop file.
plotting.cis

This plots a dataframe of fsts with bootstrapped confidence intervals.
my.read.genepop

This reads a genepop file into R
var.fst

This calculates Cockerham & Weir's Beta.
calc.betahat

This calculates beta-hat, the Fst value used in Lositan.
calc.fst

This calculates Fst.