Package: fsthet 1.0.1

fsthet: Fst-Heterozygosity Smoothed Quantiles

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) <doi:10.1093/jhered/esx048>.

Authors:Sarah P. Flanagan and Adam G. Jones

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fsthet.pdf |fsthet.html✨
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# Install 'fsthet' in R:
install.packages('fsthet', repos = c('https://spflanagan.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • bins - Example heterozygosity bins from fsthet.
  • cis - Example dataframe of smoothed quantiles from fsthet
  • cis.list - Example list of CI matrices from bootstrap output from numerical simulations
  • 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
  • quant.out - Example fsthet output based on numerical simulations

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.42 score 29 scripts 131 downloads 9 mentions 22 exports 0 dependencies

Last updated 7 years agofrom:de47813bfe. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxWARNINGOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macWARNINGOct 31 2024

Exports:allele.countscalc.actual.fstcalc.allele.freqcalc.betahatcalc.exp.hetcalc.fstcalc.thetaci.meansfhetbootfind.outliersfind.quantilesfst.bootfst.boot.meansfst.boot.onecolfst.options.printfsthetmake.binsmy.read.genepopp.bootplotting.cisremove.spacesvar.fst

Dependencies:

Using fsthet

Sarah P. Flanagan

Rendered fromfsthet-vignette.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2017-11-02
Started: 2017-11-02

Readme and manuals

Help Manual

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