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dartR.popgen (version 1.0.0)

Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Description

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) . Mijangos et al. (2022) .

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Version

Install

install.packages('dartR.popgen')

Monthly Downloads

516

Version

1.0.0

License

GPL (>= 3)

Maintainer

Bernd Gruber

Last Published

June 27th, 2024

Functions in dartR.popgen (1.0.0)

utils.outflank.plotter

Plotting functions for Fst distributions after OutFLANK
gl.run.structure

Runs a STRUCTURE analysis using a genlight object
gl.plot.structure

Plots STRUCTURE analysis results (Q-matrix)
gl.run.faststructure

Runs a faststructure analysis using a genlight object
utils.outflank

OutFLANK: An Fst outlier approach by Mike Whitlock and Katie Lotterhos, University of British Columbia.
gl.sfs

Creates a site frequency spectrum based on a dartR or genlight object
gl.run.epos

Run EPOS for Inference of Historical Population-Size Changes
utils.outflank.MakeDiploidFSTMat

Creates OutFLANK input file from individual genotype info.
utils.structure.evanno

Util function for evanno plots
utils.structure.genind2gtypes

structure util functions
zzz

Setting up the package dartR.popgen
utils.structure.run

Utility function to run Structure
gl.run.stairway2

Run Stairway Plot 2 for Demographic History Inference
gl.collapse

Collapses a distance matrix by amalgamating populations with pairwise fixed difference count less that a threshold
gl.nhybrids

Creates an input file for the program NewHybrids and runs it if NewHybrids is installed
gl.plot.faststructure

Plots fastStructure analysis results (Q-matrix)
gl.evanno

Creates an Evanno plot from a STRUCTURE run object
gl.map.structure

Maps a STRUCTURE plot using a genlight object
gl.ld.distance

Plots linkage disequilibrium against distance by population disequilibrium patterns
gl.ld.haplotype

Visualize patterns of linkage disequilibrium and identification of haplotypes
gl.blast

Aligns nucleotides sequences against those present in a target database using blastn
gl.outflank

Identifies loci under selection per population using the outflank method of Whitlock and Lotterhos (2015)
gl.LDNe

Estimates effective population size using the Linkage Disequilibrium method based on NeEstimator (V2)