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pophelper

pophelper is an R package and web app to analyse and visualise population structure. See the project website for more details. An interactive version of this package using shiny web framework is available as pophelperShiny.

Disclaimer

This R package is offered free and without warranty of any kind, either expressed or implied. I will not be held liable to you for any damage arising out of the use, modification or inability to use this program. This R package can be used, redistributed and/or modified freely for non-commercial purposes subject to the original source being properly cited. Licensed under GPL-3. Please make sure you verify all your results.

Contact

If you have an comments, suggestions, corrections or ideas on ways to improve or extend this package, feel free to contact me. Submit a report on the Github issues page.

2021 | Roy M Francis

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Version

Version

2.3.1

License

GPL-3

Issues

25

Pull Requests

1

Stars

149

Forks

37

Maintainer

Roy Francis

Last Published

December 29th, 2020

Functions in pophelper (2.3.1)

analyseQ

Analyse STRUCTURE, TESS, BAPS or BASIC text runs. Wrapper around several smaller functions.
distructExport

Generate files for DISTRUCT.
clumppExport

Generate CLUMPP output from a qlist
is.qlist

Verify if a qlist is formatted correctly.
collectClumppOutput

Collect CLUMPP output files from multiple folders
alignK

Align clusters
evannoMethodStructure

Perform the Evanno method for STRUCTURE runs.
as.qlist

Convert a qlist or qlist-like list to a valid qlist.
distructColours

Vector of 90 Distruct colours
collectRunsTess

Collect TESS run results from multiple folders
joinQ

Combine two or more qlist objects into one
readQBaps

Convert BAPS cluster files to qlist.
readQ

Convert run files (q-matrices) to qlist.
readQStructure

Convert STRUCTURE run files to qlist.
readQTess

Convert TESS cluster files to qlist.
plotQMultiline

Plot a qlist as individual-level multiline barplot
plotQ

Generate barplots from qlists.
readQTess3

Convert TESS3 R object to pophelper qlist.
readQBasic

Convert delimited text files to qlist.
readQClumpp

Convert CLUMPP format numeric text files to qlist.
sortQ

Sort runs in a qlist based on an attribute
mergeQ

Merge replicate runs of the same K
verifyGrplab

Verify a grplab dataframe
tabulateQ

Tabulate runs from a qlist
splitQ

Split a qlist into sublists by attribute
summariseQ

Summarise a tabulated dataframe