Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide
Restriction Fragment Analysis
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Documentation for package ‘dartR.popgen’ version 1.2.2
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 |