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

dart2genlightConvert DarT to genlight
foxes.glA genlight object created via the read.dart functions
gi2glConverts a genind object to genlight object
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 nexus format PAUP SVDquartets
gl2giConverts a genlight object to genind object
gl2phylipCreate a Phylip input distance matrix from a genlight (SNP)...
gl2plinkConverts a genlight object to plink file format
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
gl.collapse.pvalCollapse a fixed distance matrix by amalgamating populations...
gl.collapse.recursiveRecursively collapse a distance matrix by amalgamating...
gl.costdistancesCalculates cost distances for a given landscape (resistance...
gl.define.popDefine a new population in a genelight {adegenet} object on...
gl.dist.heatmapRepresent a distance matrix as a heatmap
gl.dist.popCalculate a distance matrix for populations defined in an...
gl.diversityCalculate diversity indices for SNPs
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 and 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 in a genlight object based on pairwise Hamming...
gl.filter.hweFilters loci that show significant departure from...
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.repavgFilter loci in a genlight {adegenet} object based on average...
gl.filter.secondariesFilter loci that represent secondary SNPs in a genlight...
gl.fixed.diffGenerate a matrix of fixed differences from a genelight or...
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 the genomic relatedness matrix
gl.grm.networkRepresents a genomic relatedness matrix as a network
gl.HoA very simple function to report observed Heterozygosity
gl.HsA very simple function to report expected Heterozygosity
gl.hwe.popFilter function to facilitate analysing of dart data
gl.ibdIsolation by distance
gl.keep.indRemove all but the specified individuals from a genelight...
gl.keep.popRemove all but specified populations from a genelight...
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.pcoaPCoA ordination (glPca)
gl.pcoa.plotBivariate plot of the results of a PCoA ordination
gl.pcoa.plot.3d3D interactive plot of the results of a PCoA ordination
gl.pcoa.popPCoA ordination of populations
gl.pcoa.screeProduce a plot of eigenvalues, standardized as percentages,...
gl.percent.freqGenerate percentage allele frequencies by locus and...
gl.plotPlotting genlight object
gl.read.dartImport DarT data into R and conver it to a genlight object
gl.read.dart.2rowImport SNP data from DArT and convert to genlight {agegenet}...
gl.read.silicodartImport presence/absence data from SilicoDArT and convert to...
gl.recalc.metricsRecalculate locus metrics when individuals or populations are...
gl.recode.indRecode individual (=specimen) labels in a genelight or genind...
gl.recode.popRecode population assignments in a genelight object...
gl.report.basesSummary of base pair frequencies
gl.report.callrateReport summary of Call Rate for loci or individuals
gl.report.hammingCalculates the pairwise Hamming distance between DArT trimmed...
gl.report.heterozygosityReports hetrozygosity
gl.report.hweReports departure from Hardy-Weinberg Equilibrium
gl.report.ldCalculates pairwise population based Linkage Disequilibirum...
gl.report.mafReport minor allele frequency (MAF) for each locus in a...
gl.report.monomorphsReport monomorphic loci, including those with all NAs
gl.report.paReport number of private alleles possessed by an individual...
gl.report.pa.popReport private alleles (and fixed alleles) per pair of...
gl.report.repavgReport summary of RepAvg, reproducibility averaged over both...
gl.report.secondariesReport loci containing secondary SNPs in a genlight...
gl.sexlinkageIdentify loci that are sex linked in specimens in a genlight...
gl.sim.indSimulates individuals based on the allele frequencies...
gl.sim.offspringSimulates a specified number of offsprings based on alleles...
gl.subsample.lociSubsample n loci from a genlight object and return as a...
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...
prob.hweExact SNP test of Hardy-Weinberg Equilibrium
read.dartImport DarT data to R
testset.glA genlight object created via the read.dart functions
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.hammingCalculates the Hamming distance between two DArT trimmed DNA...
utils.hweCalculates departure from Hardy-Weinberg Equilibrium. Utility...
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...
dartR documentation built on Nov. 26, 2018, 9:06 a.m.