| gi2gl |
Converts a genind object into a genlight object |
| gl.alf |
Calculates allele frequency of the first and second allele for each loci A very simple function to report allele frequencies |
| gl.amova |
Performs AMOVA using genlight data |
| gl.assign.grm |
Population assignment using grm |
| gl.assign.mahalanobis |
Assign an individual of unknown provenance to population based on Mahalanobis Distance |
| gl.assign.pa |
Eliminates populations as possible source populations for an individual of unknown provenance, using private alleles |
| gl.assign.pca |
Assign an individual of unknown provenance to population based on PCA |
| gl.basic.stats |
Calculates basic statistics for each loci (Hs, Ho, Fis etc.) |
| gl.blast |
Aligns nucleotides sequences against those present in a target database using blastn |
| gl.check.verbosity |
Checks the current global verbosity |
| gl.collapse |
Collapses a distance matrix by amalgamating populations with pairwise fixed difference count less that a threshold |
| gl.compliance.check |
Checks a genlight object to see if it complies with dartR expectations and amends it to comply if necessary |
| gl.costdistances |
Calculates cost distances for a given landscape (resistance matrix) |
| gl.define.pop |
Defines a new population in a genlight object for specified individuals |
| gl.diagnostics.hwe |
Provides descriptive stats and plots to diagnose potential problems with Hardy-Weinberg proportions |
| gl.diagnostics.sim |
Comparing simulations against theoretical expectations |
| gl.dist.ind |
Calculates a distance matrix for individuals defined in a genlight object |
| gl.dist.pop |
Calculates a distance matrix for populations with SNP genotypes in a genlight object |
| gl.drop.ind |
Removes specified individuals from a genlight object |
| gl.drop.loc |
Removes specified loci from a genlight object |
| gl.drop.pop |
Removes specified populations from a genlight object |
| gl.edit.recode.ind |
Creates or edits individual (=specimen) names, creates a recode_ind file and applies the changes to a genlight object |
| gl.edit.recode.pop |
Creates or edits a population re-assignment table |
| gl.evanno |
Creates an Evanno plot from a STRUCTURE run object |
| gl.fdsim |
Estimates the rate of false positives in a fixed difference analysis |
| gl.filter.allna |
Filters loci that are all NA across individuals and/or populations with all NA across loci |
| gl.filter.callrate |
Filters loci or specimens in a genlight {adegenet} object based on call rate |
| gl.filter.hamming |
Filters loci based on pairwise Hamming distance between sequence tags |
| gl.filter.heterozygosity |
Filters individuals with average heterozygosity greater than a specified upper threshold or less than a specified lower threshold |
| gl.filter.hwe |
Filters loci that show significant departure from Hardy-Weinberg Equilibrium |
| gl.filter.ld |
Filters loci based on linkage disequilibrium (LD) |
| gl.filter.locmetric |
Filters loci on the basis of numeric information stored in other$loc.metrics in a genlight {adegenet} object |
| gl.filter.maf |
Filters loci on the basis of minor allele frequency (MAF) in a genlight adegenet object |
| gl.filter.monomorphs |
Filters monomorphic loci, including those with all NAs |
| gl.filter.overshoot |
Filters loci for which the SNP has been trimmed from the sequence tag along with the adaptor |
| gl.filter.pa |
Filters loci that contain private (and fixed alleles) between two populations |
| gl.filter.parent.offspring |
Filters putative parent offspring within a population |
| gl.filter.rdepth |
Filters loci based on counts of sequence tags scored at a locus (read depth) |
| gl.filter.reproducibility |
Filters loci in a genlight {adegenet} object based on average repeatability of alleles at a locus |
| gl.filter.secondaries |
Filters loci that represent secondary SNPs in a genlight object |
| gl.filter.sexlinked |
Filters loci that are sex linked |
| gl.filter.taglength |
Filters loci in a genlight {adegenet} object based on sequence tag length |
| gl.fixed.diff |
Generates a matrix of fixed differences and associated statistics for populations taken pairwise |
| gl.fst.pop |
Calculates a pairwise Fst values for populations in a genlight object |
| gl.genleastcost |
Performs least-cost path analysis based on a friction matrix |
| gl.grm |
Calculates an identity by descent matrix |
| gl.grm.network |
Represents a genomic relationship matrix (GRM) as a network |
| gl.He |
Estimates expected Heterozygosity |
| gl.Ho |
Estimates observed Heterozygosity |
| gl.hwe.pop |
Performs Hardy-Weinberg tests over loci and populations |
| gl.ibd |
Performs isolation by distance analysis |
| gl.impute |
Imputates missing data |
| gl.install.vanilla.dartR |
Installs all required packages for using all functions available in dartR |
| gl.join |
Combines two genlight objects |
| gl.keep.ind |
Removes all but the specified individuals from a genlight object |
| gl.keep.loc |
Removes all but the specified loci from a genlight object |
| gl.keep.pop |
Removes all but the specified populations from 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.LDNe |
Estimates effective population size using the Linkage Disequilibrium method based on NeEstimator (V2) |
| gl.list.reports |
Prints dartR reports saved in tempdir |
| gl.load |
Loads an object from compressed binary format produced by gl.save() |
| gl.make.recode.ind |
Creates a proforma recode_ind file for reassigning individual (=specimen) names |
| gl.make.recode.pop |
Creates a proforma recode_pop_table file for reassigning population names |
| gl.map.interactive |
Creates an interactive map (based on latlon) from a genlight object |
| gl.map.structure |
Maps a STRUCTURE plot using a genlight object |
| gl.merge.pop |
Merges two or more populations in a genlight object into one population |
| 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.pcoa |
Ordination applied to genotypes in a genlight object (PCA), in an fd object, or to a distance matrix (PCoA) |
| gl.pcoa.plot |
Bivariate or trivariate plot of the results of an ordination generated using gl.pcoa() |
| gl.percent.freq |
Generates percentage allele frequencies by locus and population |
| gl.play.history |
Replays the history and applies it to a genlight object |
| gl.plot.heatmap |
Represents a distance matrix as a heatmap |
| gl.plot.network |
Represents a distance or dissimilarity matrix as a network |
| gl.plot.structure |
Plots STRUCTURE analysis results (Q-matrix) |
| gl.print.history |
Prints history of a genlight object |
| gl.print.reports |
Prints dartR reports saved in tempdir |
| gl.propShared |
Calculates a similarity (distance) matrix for individuals on the proportion of shared alleles |
| gl.random.snp |
Randomly changes the allocation of 0's and 2's in a genlight object |
| gl.read.csv |
Reads SNP data from a csv file into a genlight object |
| gl.read.dart |
Imports DArT data into dartR and converts it into a genlight object |
| gl.read.fasta |
Reads FASTA files and converts them to genlight object |
| gl.read.silicodart |
Imports presence/absence data from SilicoDArT to genlight {agegenet} format (ploidy=1) |
| gl.read.vcf |
Converts a vcf file into a genlight object |
| gl.reassign.pop |
Assigns an individual metric as pop in a genlight {adegenet} object |
| gl.recalc.metrics |
Recalculates locus metrics when individuals or populations are deleted from a genlight {adegenet} object |
| gl.recode.ind |
Recodes individual (=specimen = sample) labels in a genlight object |
| gl.recode.pop |
Recodes population assignments in a genlight object |
| gl.rename.pop |
Renames a population in a genlight object |
| gl.report.bases |
Reports summary of base pair frequencies |
| gl.report.callrate |
Reports summary of Call Rate for loci or individuals |
| gl.report.diversity |
Calculates diversity indexes for SNPs |
| gl.report.hamming |
Calculates the pairwise Hamming distance between DArT trimmed DNA sequences |
| gl.report.heterozygosity |
Reports observed, expected and unbiased heterozygosities and FIS (inbreeding coefficient) by population or by individual from SNP data |
| gl.report.hwe |
Reports departure from Hardy-Weinberg proportions |
| gl.report.ld |
Calculates pairwise population based Linkage Disequilibrium across all loci using the specified number of cores |
| gl.report.ld.map |
Calculates pairwise linkage disequilibrium by population |
| gl.report.locmetric |
Reports summary of the slot $other$loc.metrics |
| gl.report.maf |
Reports minor allele frequency (MAF) for each locus in a SNP dataset |
| gl.report.monomorphs |
Reports monomorphic loci |
| gl.report.overshoot |
Reports loci for which the SNP has been trimmed from the sequence tag along with the adaptor |
| gl.report.pa |
Reports private alleles (and fixed alleles) per pair of populations |
| gl.report.parent.offspring |
Identifies putative parent offspring within a population |
| gl.report.rdepth |
Reports summary of Read Depth for each locus |
| gl.report.reproducibility |
Reports summary of RepAvg (repeatability averaged over both alleles for each locus) or reproducibility (repeatability of the scores for fragment presence/absence) |
| gl.report.secondaries |
Reports loci containing secondary SNPs in sequence tags and calculates number of invariant sites |
| gl.report.sexlinked |
Identifies loci that are sex linked |
| gl.report.taglength |
Reports summary of sequence tag length across loci |
| gl.run.structure |
Runs a STRUCTURE analysis using a genlight object |
| gl.sample |
Samples individuals from populations |
| gl.save |
Saves an object in compressed binary format for later rapid retrieval |
| gl.select.colors |
Selects colors from one of several palettes and output as a vector |
| gl.select.shapes |
Selects shapes from the base R shape palette and outputs as a vector |
| gl.set.verbosity |
Sets the default verbosity level |
| gl.sfs |
Creates a site frequency spectrum based on a dartR or genlight object |
| gl.sim.create_dispersal |
Creates a dispersal file as input for the function gl.sim.WF.run |
| gl.sim.emigration |
Simulates emigration between populations |
| gl.sim.ind |
Simulates individuals based on the allele frequencies provided via a genlight object. |
| gl.sim.mutate |
Simulates mutations within a genlight object |
| gl.sim.offspring |
Simulates a specified number of offspring based on alleles provided by potential father(s) and mother(s) |
| gl.sim.WF.run |
Runs Wright-Fisher simulations |
| gl.sim.WF.table |
Creates the reference table for running gl.sim.WF.run |
| gl.smearplot |
Smear plot of SNP or presence/absence (SilicoDArT) data |
| gl.sort |
re-sorts genlight objects |
| gl.spatial.autoCorr |
Spatial autocorrelation following Smouse and Peakall 1999 |
| gl.subsample.loci |
Subsamples n loci from a genlight object and return it as a genlight object |
| gl.test.heterozygosity |
Tests the difference in heterozygosity between populations taken pairwise |
| gl.tree.nj |
Outputs an nj tree to summarize genetic similarity among populations |
| gl.write.csv |
Writes out data from a genlight object to csv file |
| gl2bayescan |
Converts a genlight object into a format suitable for input to Bayescan |
| gl2bpp |
Converts a genlight object into a format suitable for input to the BPP program |
| gl2demerelate |
Creates a dataframe suitable for input to package {Demerelate} from a genlight {adegenet} object |
| gl2eigenstrat |
Converts a genlight object into eigenstrat format |
| gl2fasta |
Concatenates DArT trimmed sequences and outputs a FASTA file |
| gl2faststructure |
Converts a genlight object into faststructure format (to run faststructure elsewhere) |
| gl2gds |
Converts a genlight object into gds format |
| gl2genalex |
Converts a genlight object into a format suitable for input to genalex |
| gl2genepop |
Converts a genlight object into genepop format (and file) |
| gl2geno |
Converts a genlight object to geno format from package LEA |
| gl2gi |
Converts a genlight object to genind object |
| gl2hiphop |
Converts a genlight objects into hiphop format |
| gl2phylip |
Creates a Phylip input distance matrix from a genlight (SNP) {adegenet} object |
| gl2plink |
Converts a genlight object into PLINK format |
| gl2related |
Converts a genlight object to format suitable to be run with Coancestry |
| gl2sa |
Converts genlight objects to the format used in the SNPassoc package |
| gl2sfs |
Converts a genlight object into a sfs input file |
| gl2shp |
Converts a genlight object to ESRI shapefiles or kml files |
| gl2snapp |
Converts a genlight object to nexus format suitable for phylogenetic analysis by SNAPP (via BEAUti) |
| gl2structure |
Converts a genlight object to STRUCTURE formatted files |
| gl2svdquartets |
Converts a genlight object to nexus format PAUP SVDquartets |
| gl2treemix |
Converts a genlight object to a treemix input file |
| gl2vcf |
Converts a genlight object into vcf format |
| utils.assignment |
Population assignment probabilities |
| utils.assignment_2 |
Population assignment probabilities |
| utils.assignment_3 |
Population assignment probabilities |
| utils.assignment_4 |
Population assignment probabilities |
| utils.basic.stats |
Calculates mean observed heterozygosity, mean expected heterozygosity and Fis per locus, per population and various population differentiation measures |
| utils.check.datatype |
Utility function to check the class of an object passed to a function |
| utils.dart2genlight |
Converts DarT to genlight |
| utils.dist.binary |
Calculates a distance matrix for individuals defined in a dartR genlight object using binary P/A data (SilicoDArT) |
| utils.dist.ind.snp |
Calculates a distance matrix for individuals defined in a dartR genlight object using SNP data (DArTseq) |
| utils.flag.start |
A utility script to flag the start of a script |
| utils.hamming |
Calculates the Hamming distance between two DArT trimmed DNA sequences |
| utils.het.pop |
Calculates expected mean expected heterozygosity per population |
| utils.jackknife |
Conducts jackknife resampling using a genlight object |
| utils.n.var.invariant |
A utility script to calculate the number of variant and invariant sites by locus |
| 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.read.dart |
Imports DarT data to R |
| utils.recalc.avgpic |
A utility script to recalculate the OneRatioRef, OneRatioSnp, PICRef, PICSnp, and AvgPIC by locus after some individuals or populations have been deleted. |
| utils.recalc.callrate |
A utility script to recalculate the callrate by locus after some populations have been deleted |
| utils.recalc.freqhets |
A utility script to recalculate the frequency of the heterozygous SNPs by locus after some populations have been deleted |
| utils.recalc.freqhomref |
A utility script to recalculate the frequency of the homozygous reference SNP by locus after some populations have been deleted |
| utils.recalc.freqhomsnp |
A utility script to recalculate the frequency of the homozygous alternate SNP by locus after some populations have been deleted |
| utils.recalc.maf |
A utility script to recalculate the minor allele frequency by locus, typically after some populations have been deleted |
| utils.reset.flags |
A utility script to reset to FALSE (or TRUE) the locus metric flags after some individuals or populations have been deleted. |
| utils.spautocor |
Spatial autocorrelation coefficient calculations |
| utils.structure.evanno |
Util function for evanno plots |
| utils.structure.genind2gtypes |
structure util functions |
| utils.structure.run |
Utility function to run Structure |
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