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poolfstat  

Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data
View on CRAN: Click here


Download and install poolfstat package within the R console
Install from CRAN:
install.packages("poolfstat")

Install from Github:
library("remotes")
install_github("cran/poolfstat")

Install by package version:
library("remotes")
install_version("poolfstat", "2.2.0")



Attach the package and use:
library("poolfstat")
Maintained by
Mathieu Gautier
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2018-03-14
Latest Update: 2023-03-22
Description:
Functions for the computation of f- and D-statistics (estimation of 'Fst', Patterson's 'F2', 'F3', 'F3*', 'F4' and D parameters) in population genomics studies from allele count or Pool-Seq read count data and for the fitting, building and visualization of admixture graphs. The package also includes several utilities to manipulate Pool-Seq data stored in standard format (e.g., such as 'vcf' files or 'rsync' files generated by the the 'PoPoolation' software) and perform conversion to alternative format (as used in the 'BayPass' and 'SelEstim' software). As of version 2.0, the package also includes utilities to manipulate standard allele count data (e.g., stored in 'TreeMix', 'BayPass' or 'SelEstim' format).
How to cite:
Mathieu Gautier (2018). poolfstat: Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data. R package version 2.2.0, https://cran.r-project.org/web/packages/poolfstat
Previous versions and publish date:
0.0.1 (2018-03-14 12:36), 1.0.0 (2018-09-14 21:20), 1.1.0 (2019-06-20 17:00), 1.1.1 (2019-10-22 11:30), 1.2.0 (2020-11-04 17:20), 2.0.0 (2021-05-27 11:20), 2.1.1 (2022-05-02 18:10), 2.1.2 (2023-03-22 23:00)
Other packages that cited poolfstat R package
View poolfstat citation profile
Other R packages that poolfstat depends, imports, suggests or enhances
Functions, R codes and Examples using the poolfstat R package
Some associated functions: add.leaf . bjack_cov . compare.fitted.fstats . compute.f4ratio . compute.fstats . compute.pairwiseFST . computeFST . compute_Ddenom . compute_Ddenom_bjmeans . compute_F2_bjmeans . compute_F3fromF2 . compute_F3fromF2samples . compute_F4DfromF2samples . compute_F4fromF2 . compute_F4fromF2samples . compute_H1 . compute_Q2 . compute_Q_bjmeans . compute_QmatfromF2samples . compute_blockDdenom . countdata-class . countdata.subset . extract_allele_names . extract_nonvscan_counts . extract_vscan_counts . find.tree.popset . find_indelneighbor_idx . fit.graph . fitted.graph-class . fstats-class . generate.graph.params . generate.jackknife.blocks . generateF3names . generateF4names . genobaypass2countdata . genobaypass2pooldata . genoselestim2pooldata . genotreemix2countdata . graph.builder . graph.params-class . graph.params2qpGraphFiles . graph.params2symbolic.fstats . heatmap-pairwisefst-method . is.countdata . is.fitted.graph . is.fstats . is.graph.params . is.pairwisefst . is.pooldata . make.example.files . pairwisefst-class . plot-fitted.graph-method . plot-fstats-method . plot-graph.params-method . plot-pairwisefst-method . plot_fstats . pooldata-class . pooldata.subset . pooldata2diyabc . pooldata2genobaypass . pooldata2genoselestim . poolfstat . poppair_idx . popsync2pooldata . randomallele.pca . rooted.njtree.builder . scan_allele_info . show-countdata-method . show-fitted.graph-method . show-fstats-method . show-graph.params-method . show-pairwisefst-method . show-pooldata-method . vcf2pooldata . 
Some associated R codes: RcppExports.R . add.leaf.R . compare.fitted.fstats.R . compute.F4ratio.R . compute.fstats.R . compute.pairwiseFST.R . computeFST.R . countdata.subset.R . find.tree.popset.R . fit.graph.R . generate.graph.params.R . generate.jacknife.blocks.R . genobaypass2countdata.R . genobaypass2pooldata.R . genoselestim2pooldata.R . genotreemix2countdata.R . graph.builder.R . graph.params2qpGraphFiles.R . graph.params2symbolicfstats.R . is.countdata.R . is.fitted.graph.R . is.graph.params.R . is.pooldata.R . make.example.files.R . outjects.R . plot_fstats.R . pooldata.subset.R . pooldata2diyabc.R . pooldata2genobaypass.R . pooldata2genoselestim.R . poolfstat-package.R . popsync2pooldata.R . randomallele.pca.R . rooted.njtree.builder.R . vcf2pooldata.R .  Full poolfstat package functions and examples
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