Function reference • dartR

All functions

bandicoot.gl: A genlight object created via the read.dart functions

cbind(<dartR>): adjust cbind for dartR

gi2gl(): Converts a genind object into a genlight object

gl.He(): Estimates expected Heterozygosity

gl.Ho(): Estimates observed Heterozygosity

gl.LDNe(): Estimates effective population size using the Linkage Disequilibrium method based on NeEstimator (V2)

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 {adegenet} object

gl.drop.loc(): Removes specified loci from a genlight {adegenet} 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.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 {adegenet} object

gl.keep.loc(): Removes all but the specified loci from a genlight {adegenet} 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.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.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.WF.run(): Runs Wright-Fisher simulations

gl.sim.WF.table(): Creates the reference table for running gl.sim.WF.run

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.smearplot(): Smear plot of SNP or presence/absence (SilicoDArT) data

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 formated 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

interactive_reference(): Shiny app for the input of the reference table for the simulations

interactive_sim_run(): Shiny app for the input of the simulations variables

is.fixed(): Tests if two populations are fixed at a given locus

platy: Example data set as text file to be imported into a genlight object

possums.gl: A simulated genlight object created to run a landscape genetic example

rbind(<dartR>): adjust rbind for dartR

`[`(<dartR>,<ANY>,<ANY>,<ANY>): indexing dartR objects correctly...

testset.gl: A genlight object created via the gl.read.dart function

testset.gs: A genlight object created via the gl.read.silicodart function

testset_SNPs_2Row: Testfile in DArT format (as provided by DArT)

testset_metadata: Metadata file. Can be integrated via the dart2genlight function.

testset_pop_recode: Recode file to be used with the function.

theme_dartR(): dartR theme

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 Fst across all populations

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.MakeDiploidFSTMat(): Creates OutFLANK input file from individual genotype info.

utils.outflank(): OutFLANK: An Fst outlier approach by Mike Whitlock and Katie Lotterhos, University of British Columbia.

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

zzz: Setting up the package