Package: dartR.popgen 1.0.0

Bernd Gruber

dartR.popgen:Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Facilitates the analysis of SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. 'dartR.popgen' provides a suit of functions to analyse such data in a population genetics context. It provides several functions to calculate population genetic metrics and to study population structure. Quite a few functions need additional software to be able to run (gl.run.structure(), gl.blast(), gl.LDNe()). You find detailed description in the help pages how to download and link the packages so the function can run the software. 'dartR.popgen' is part of the the 'dartRverse' suit of packages. Gruber et al. (2018) <doi:10.1111/1755-0998.12745>. Mijangos et al. (2022) <doi:10.1111/2041-210X.13918>.

Authors:Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Carlo Pacioni [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb], Eric Archer [ctb]

dartR.popgen_1.0.0.tar.gz
dartR.popgen_1.0.0.tar.gz(r-4.5-noble)dartR.popgen_1.0.0.tar.gz(r-4.4-noble)
dartR.popgen_1.0.0.tgz(r-4.4-emscripten)dartR.popgen_1.0.0.tgz(r-4.3-emscripten)
dartR.popgen.pdf |dartR.popgen.html✨
dartR.popgen/json (API)

# InstalldartR.popgen in R:
install.packages('dartR.popgen',repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/green-striped-gecko/dartr/issues

22 exports 0.23 score 93 dependencies 305 downloads

Last updated 8 days agofrom:a86c689ce6

Exports:gl.blastgl.collapsegl.evannogl.ld.distancegl.ld.haplotypegl.LDNegl.map.structuregl.nhybridsgl.outflankgl.plot.faststructuregl.plot.structuregl.run.eposgl.run.faststructuregl.run.stairway2gl.run.structuregl.sfsutils.outflankutils.outflank.MakeDiploidFSTMatutils.outflank.plotterutils.structure.evannoutils.structure.genind2gtypesutils.structure.run

Dependencies:ade4adegenetapebase64encbootbslibcachemcliclustercodetoolscolorspacecommonmarkcpp11crayondartR.basedartR.datadata.tabledigestdoParalleldplyrfansifarverfastmapfontawesomeforeachfsfurrrfuturegdsfmtgenericsggdendroggplot2globalsgluegridExtragtablehtmltoolshttpuvigraphisobanditeratorsjquerylibjsonlitelabelinglaterlatticelifecyclelistenvmagrittrMASSMatrixmemoisemgcvmimemunsellnlmeparallellypatchworkpegaspermutepillarpixmappkgconfigplyrpromisespurrrR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangsassscalessegmentedseqinrshinySNPRelatesourcetoolsspStAMPPstringistringrtibbletidyrtidyselectutf8vctrsveganviridisLitewithrxtable

Readme and manuals

Help Manual

Help pageTopics
Aligns nucleotides sequences against those present in a target database using blastngl.blast
Collapses a distance matrix by amalgamating populations with pairwise fixed difference count less that a thresholdgl.collapse
Creates an Evanno plot from a STRUCTURE run objectgl.evanno
Plots linkage disequilibrium against distance by population disequilibrium patternsgl.ld.distance
Visualize patterns of linkage disequilibrium and identification of haplotypesgl.ld.haplotype
Estimates effective population size using the Linkage Disequilibrium method based on NeEstimator (V2)gl.LDNe
Maps a STRUCTURE plot using a genlight objectgl.map.structure
Creates an input file for the program NewHybrids and runs it if NewHybrids is installedgl.nhybrids
Identifies loci under selection per population using the outflank method of Whitlock and Lotterhos (2015)gl.outflank
Plots fastStructure analysis results (Q-matrix)gl.plot.faststructure
Plots STRUCTURE analysis results (Q-matrix)gl.plot.structure
Run EPOS for Inference of Historical Population-Size Changesgl.run.epos
Runs a faststructure analysis using a genlight objectgl.run.faststructure
Run Stairway Plot 2 for Demographic History Inferencegl.run.stairway2
Runs a STRUCTURE analysis using a genlight objectgl.run.structure
Creates a site frequency spectrum based on a dartR or genlight objectgl.sfs
OutFLANK: An Fst outlier approach by Mike Whitlock and Katie Lotterhos, University of British Columbia.utils.outflank
Creates OutFLANK input file from individual genotype info.utils.outflank.MakeDiploidFSTMat
Plotting functions for Fst distributions after OutFLANKutils.outflank.plotter
Util function for evanno plotsutils.structure.evanno
structure util functionsutils.structure.genind2gtypes
Utility function to run Structureutils.structure.run