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

## Documentation for package ‘dartR.popgen’ version 1.2.2

- DESCRIPTION file.

## Help Pages

gl.blast | Aligns nucleotides sequences against those present in a target database using blastn
gl.check.panel | Check a snp panel for a specified parameter
gl.collapse | Collapses a distance matrix by amalgamating populations with pairwise fixed difference count less that a threshold
gl.evanno | Creates an Evanno plot from a STRUCTURE run object
gl.find.genes.for.loci | Map loci (SNPs) to the nearest gene feature from a GFF
gl.find.loci.in.genes | Find loci that fall within genes matching a pattern (from a GFF)
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.LDNe | Estimates effective population size using the Linkage Disequilibrium method based on NeEstimator (V2)
gl.map.popcluster | Maps a PopCluster plot using a genlight object
gl.map.snmf | Maps a snmf plot using a genlight object
gl.map.structure | Maps a STRUCTURE plot using a genlight object
gl.nhybrids | Creates an input file for the program NewHybrids and runs it if NewHybrids is installed
gl.outflank | Identifies loci under selection per population using the outflank method of Whitlock and Lotterhos (2015)
gl.plot.faststructure | Plots fastStructure analysis results (Q-matrix)
gl.plot.popcluster | Plots PopCluster analysis results (Admixture Model)
gl.plot.snmf | Plots ancestry coefficient from snmf
gl.plot.structure | Plots STRUCTURE analysis results (Q-matrix)
gl.read.structure | Read output files produced by the program STRUCTURE
gl.run.epos | Run EPOS for Inference of Historical Population-Size Changes
gl.run.faststructure | Runs a faststructure analysis using a genlight object
gl.run.popcluster | Runs a PopCluster analysis using a genlight object
gl.run.snmf | Creates an input file for the function snmf (package LEA) and runs it if package LEA is installed.
gl.run.stairway2 | Run Stairway Plot 2 for Demographic History Inference
gl.run.structure | Runs a STRUCTURE analysis using a genlight object
gl.select.panel | Select Loci Panel Based on Various Methods
gl.sfs | Creates a site frequency spectrum based on a dartR or genlight object
gl.TajimasD | Calculation of Tajima's D
utils.get.allele.freq | utils.get.allele.freq
utils.outflank | OutFLANK: An Fst outlier approach by Mike Whitlock and Katie Lotterhos, University of British Columbia.
utils.outflank.MakeDiploidFSTMat | Creates OutFLANK input file from individual genotype info.
utils.outflank.plotter | Plotting functions for Fst distributions after OutFLANK
utils.structure.evanno | Util function for evanno plots
utils.structure.genind2gtypes | structure util functions
utils.structure.run | Utility function to run Structure