Man pages for dartR
Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis

bandicoot.glA genlight object created via the read.dart functions
gi2glConverts a genind object to genlight object
gl2bayescanConvert a genlight object to format suitable for input to...
gl2demerelateCreate a dataframe suitable for input to package {Demerelate}...
gl2fastaConcatenates DArT trimmed sequences and outputs a fastA file.
gl2faststructureExport DArT genlight object {adegenet} to faststructure...
gl2gdsConvert a genlight object to gds format
gl2genalexConvert a genlight object to format suitable for input to...
gl2giConverts a genlight object to genind object
gl2hiphopConverts genlight objects to hiphop format
gl2phylipCreate a Phylip input distance matrix from a genlight (SNP)...
gl2plinkConverts a genlight object to PLINK file format
gl2relatedConvert a genlight object to format suitable to be run with...
gl2saConvert genlight objects to the format used in the SNPassoc...
gl2shpConvert genlight objects to ESRI shapefiles or kml files
gl2snappConvert a genlight object to nexus format suitable for...
gl2structureConverts genlight objects to STRUCTURE formated files
gl2svdquartetsConvert a genlight object to nexus format PAUP SVDquartets
gl2treemixConvert a genlight object to a treemix input file
gl.alfCalculates allele frequency of the first and second allele...
gl.amovaPerforms and AMOVA using genlight data.
gl.assignAssign an individual of unknown provenance to population
gl.basic.statsCalculates basic statistics for each loci (Hs, Ho, Fis etc.)
gl.collapseCollapse a distance matrix by amalgamating populations with...
gl.collapse.pvalCollapse a fixed distance matrix by amalgamating populations...
gl.collapse.recursiveRecursively collapse a distance matrix by amalgamating...
gl.compliance.checkChecks a gl object to see if it complies with dartR...
gl.costdistancesCalculates cost distances for a given landscape (resistance...
gl.define.popDefine a new population in a genlight {adegenet} object on...
gl.dist.indCalculate a distance matrix for individuals defined in an...
gl.dist.popCalculate a distance matrix for populations defined in an...
gl.drop.indRemove specified individuals from a genelight {adegenet}...
gl.drop.locRemove specified loci from a genelight {adegenet} object
gl.drop.popRemove specified populations from a genelight {adegenet}...
gl.edit.recode.indCreate or edit a individual (=specimen) names, create an...
gl.edit.recode.popCreate or edit a population re-assignment table
gl.filter.callrateFilter loci or specimens in a genlight {adegenet} object...
gl.filter.cloneidFilter for CloneID to select only unique SNPs
gl.filter.hammingFilters loci based on pairwise Hamming distance between...
gl.filter.heterozygosityFilters individuals with average heterozygosity greater than...
gl.filter.hweFilters loci that show significant departure from...
gl.filter.locmetricFilter loci on the basis of numeric information stored in...
gl.filter.mafFilter loci on the basis of minor allele frequency (MAF) in a...
gl.filter.monomorphsRemove monomorphic loci, including those with all NAs
gl.filter.overshootFilters loci for which the SNP has been trimmed from the...
gl.filter.paFilter loci that contain private (and fixed alleles) between...
gl.filter.parent.offspringFilter putative parent offspring within a population
gl.filter.rdepthFilter loci based on counts of sequence tags scored at a...
gl.filter.RepAvgFilter loci in a genlight {adegenet} object based on average...
gl.filter.reproducibilityFilter loci in a genlight {adegenet} object based on average...
gl.filter.secondariesFilter loci that represent secondary SNPs in a genlight...
gl.filter.sexlinkedIdentify loci that are sex linked in specimens in a genlight...
gl.filter.taglengthFilter loci in a genlight {adegenet} object based on sequence...
gl.fixed.diffGenerate a matrix of fixed differences
gl.fst.popCalculate a pairwise fst values for populations in a genlight...
gl.gene.freqCalculate a statistic for each locus by group An internal...
gl.genleastcostLeast-cost path analysis based on a friction matrix
gl.grmCalculates an identity by descent matrix
gl.grm.networkRepresents a genomic relatedness matrix as a network
gl.HeA very simple function to report expected Heterozygosity
gl.HoA very simple function to report observed Heterozygosity
gl.hwe.popFunction to run Hardy-Weinberg tests over each loci and...
gl.ibdIsolation by distance
gl.install.vanilla.dartRThis functions installs all required packages for using all...
gl.joinCombines two genlight objects
gl.keep.indRemove all but the specified individuals from a genelight...
gl.keep.locRemove all but the specified loci from a genelight {adegenet}...
gl.keep.popRemove all but specified populations from a genelight...
gl.loadRetrieves an object in compressed binary format earlier saved...
gl.make.recode.indCreate a proforma recode_ind file for reassigning individual...
gl.make.recode.popCreate a proforma recode_pop_table file for reassigning...
gl.map.interactiveCreates an interactive map (based on latlong) from a genlight...
gl.merge.popMerge two or more populations in a genelight {adegenet}...
gl.nhybridsCreate an input file for the program NewHybrids and run it if...
gl.outflankFunction to identify loci under selection per population...
gl.pcoaOrdination applied to genotypes in a genlight object (PCA),...
gl.pcoa.plotBivariate plot of the results of an ordination generated...
gl.pcoa.plot.3d3D interactive plot of the results of a PCoA ordination
gl.pcoa.screeProduce a plot of eigenvalues, standardized as percentages,...
gl.percent.freqGenerate percentage allele frequencies by locus and...
gl.play.historyReplays the history and applies it to a genlight object
gl.plotPlotting genlight object as a smear plot (loci by individuals...
gl.plot.heatmapRepresent a distance matrix as a heatmap
gl.plot.networkRepresents a distance or dissimilarity matrix as a network
gl.print.historyPrints history of a genlight object
gl.propSharedCalculate a similarity(distance) matrix for individuals on...
gl.read.csvRead SNP data from a csv file into a genlight object
gl.read.dartImport DarT data into R and conver it to a genlight object
gl.read.silicodartImport presence/absence data from SilicoDArT to genlight...
gl.read.vcfConverts a vcf file into a genlight object
gl.reassign.popAssign a individual metric as pop in a genlight {adegenet}...
gl.recalc.metricsRecalculate locus metrics when individuals or populations are...
gl.recode.indRecode individual (=specimen = sample) labels in a genelight...
gl.recode.popRecode population assignments in a genlight object {adegenet}
gl.report.basesSummary of base pair frequencies
gl.report.callrateReport summary of Call Rate for loci or individuals
gl.report.diversityCalculate diversity indices for SNPs
gl.report.hammingCalculates the pairwise Hamming distance between DArT trimmed...
gl.report.heterozygosityReports observed and expected heterozygosity by population or...
gl.report.hweReports departure from Hardy-Weinberg Equilibrium
gl.report.ldCalculates pairwise population based Linkage Disequilibirum...
gl.report.locmetricReport summary of the slot $other$loc.metrics
gl.report.mafReport minor allele frequency (MAF) for each locus in a SNP...
gl.report.monomorphsReport monomorphic loci
gl.report.overshootReports loci for which the SNP has been trimmed from the...
gl.report.paReport private alleles (and fixed alleles) per pair of...
gl.report.parent.offspringIdentify putative parent offspring within a population
gl.report.rdepthReport summary of Read Depth for each locus
gl.report.RepAvgReport summary of RepAvg averaged over both alleles for each...
gl.report.reproducibilityReport summary of RepAvg (repeatability averaged over both...
gl.report.secondariesReport loci containing secondary SNPs in sequence tags
gl.report.sexlinkedIdentify loci that are sex linked in specimens in a genlight...
gl.report.taglengthReport summary of sequence tag length across loci in a...
gl.saveSave an object in compressed binary format for later rapid...
gl.set.verbositySet the default verbosity level
gl.sim.indSimulates individuals based on the allele frequencies...
gl.sim.offspringSimulates a specified number of offsprings based on alleles...
gl.stockRGenerate a SNP matrix from a genlight {adegenet} object for...
gl.subsample.lociSubsample n loci from a genlight object and return as a...
gl.test.heterozygosityTests the difference in heterozyosity between populations...
gl.tree.njOutput an nj tree to summarize genetic similarity among...
gl.utils.fdsimEstimate the rate of false positives in a fixed difference...
gl.write.csvWrite out data from a gl object adegenet to csv file
is.fixedTest to see if two populations are fixed at a given locus
platyExample data set as text file to be imported into a genlight...
possums.glA simulated genlight object created to run a landscape...
testset.glA genlight object created via the gl.read.dart function
testset.gsA genlight object created via the gl.read.silicodart function
testset_metadataMetadata file. Can be integrated via the dart2genlight...
testset_pop_recodeRecode file to be used with the function.
testset_SNPs_2RowTestfile in DArT format (as provided by DArT)
util.outflankOutFLANK: An Fst outlier approach by Mike Whitlock and Katie...
util.outflank.MakeDiploidFSTMatCreates OutFLANK input file from individual genotype info.
util.outflank.plotterPlotting functions for Fst distributions after OutFLANK This...
utils.dart2genlightConvert DarT to genlight
utils.dist.binaryCalculate a distance matrix for individuals defined in an...
utils.hammingCalculates the Hamming distance between two DArT trimmed DNA...
utils.hweCalculates departure from Hardy-Weinberg Equilibrium. Utility...
utils.outflankOutFLANK: An Fst outlier approach by Mike Whitlock and Katie...
utils.outflank.MakeDiploidFSTMatCreates OutFLANK input file from individual genotype info.
utils.outflank.plotterPlotting functions for Fst distributions after OutFLANK This...
utils.pa.indReport number of private alleles possessed by an individual...
utils.prob.hweExact SNP test of Hardy-Weinberg Equilibrium
utils.read.dartImport DarT data to R
utils.recalc.avgpicA utility script to recalculate the OneRatioRef, OneRatioSnp,...
utils.recalc.callrateA utility script to recalculate the callrate by locus after...
utils.recalc.freqhetsA utility script to recalculate the the frequency of the...
utils.recalc.freqhomrefA utility script to recalculate the the frequency of the...
utils.recalc.freqhomsnpA utility script to recalculate the the frequency of the...
utils.recalc.mafA utility script to recalculate the the minor allele...
utils.reset.flagsA utility script to reset to FALSE (or TRUE) the locus metric...
dartR documentation built on May 29, 2021, 1:08 a.m.