Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis


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Documentation for package ‘dartR’ version 1.9.9.1

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B G I P T U

-- B --

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

-- G --

gi2gl Converts a genind object to 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 and AMOVA using genlight data.
gl.assign Assign an individual of unknown provenance to population
gl.basic.stats Calculates basic statistics for each loci (Hs, Ho, Fis etc.)
gl.collapse Collapse a distance matrix by amalgamating populations with pairwise fixed difference count less that a threshold
gl.collapse.pval Collapse a fixed distance matrix by amalgamating populations for which pairwise fixed differences are not significant
gl.collapse.recursive Recursively collapse a distance matrix by amalgamating populations
gl.compliance.check Checks a gl object to see if it complies with dartR expectations, and amends to comply if necessary
gl.costdistances Calculates cost distances for a given landscape (resistance matrix)
gl.define.pop Define a new population in a genlight {adegenet} object on the basis of specified individuals
gl.dist.ind Calculate a distance matrix for individuals defined in an {adegenet} genlight object
gl.dist.pop Calculate a distance matrix for populations defined in an {adegenet} genlight object
gl.drop.ind Remove specified individuals from a genelight {adegenet} object
gl.drop.loc Remove specified loci from a genelight {adegenet} object
gl.drop.pop Remove specified populations from a genelight {adegenet} object
gl.edit.recode.ind Create or edit a individual (=specimen) names, create an recode_ind file amd apply the changes to a genlight object.
gl.edit.recode.pop Create or edit a population re-assignment table
gl.filter.callrate Filter loci or specimens in a genlight {adegenet} object based on call rate
gl.filter.cloneid Filter for CloneID to select only unique SNPs
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.locmetric Filter loci on the basis of numeric information stored in other$loc.metrics in a genlight {adegenet} object
gl.filter.maf Filter loci on the basis of minor allele frequency (MAF) in a genlight adegenet object
gl.filter.monomorphs Remove 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 Filter loci that contain private (and fixed alleles) between two populations.
gl.filter.parent.offspring Filter putative parent offspring within a population
gl.filter.rdepth Filter loci based on counts of sequence tags scored at a locus (read depth)
gl.filter.RepAvg Filter loci in a genlight {adegenet} object based on average repeatability of alleles at a locus
gl.filter.reproducibility Filter loci in a genlight {adegenet} object based on average repeatability of alleles at a locus
gl.filter.secondaries Filter loci that represent secondary SNPs in a genlight {adegenet} object
gl.filter.sexlinked Identify loci that are sex linked in specimens in a genlight 'adegenet' object
gl.filter.taglength Filter loci in a genlight {adegenet} object based on sequence tag length
gl.fixed.diff Generate a matrix of fixed differences
gl.fst.pop Calculate a pairwise fst values for populations in a genlight object
gl.gene.freq Calculate a statistic for each locus by group An internal function essentially to convey readability to rather contorted R code. It takes as input a genlight {adegenet} object with an index variable (say, population) and calculates the selected statistic for each locus, broken down by the groups defined by the index variable.
gl.genleastcost Least-cost path analysis based on a friction matrix
gl.grm Calculates an identity by descent matrix
gl.grm.network Represents a genomic relatedness matrix as a network
gl.He A very simple function to report expected Heterozygosity
gl.Ho A very simple function to report observed Heterozygosity
gl.hwe.pop Function to run Hardy-Weinberg tests over each loci and population
gl.ibd Isolation by distance
gl.install.vanilla.dartR This functions installs all required packages for using all functions available in dartR The function compares the installed packages with the the currently available ones on cran. Be aware this function only works if a version of dartR is already installed on your system. You can choose if you also want to have a specific version of dartR installed ("CRAN", "master" or "dev" ). "master" and "dev" are installed from Github. Be aware the dev version from github is not fully tested and most certainly will contain untested functions.
gl.join Combines two genlight objects
gl.keep.ind Remove all but the specified individuals from a genelight {adegenet} object
gl.keep.loc Remove all but the specified loci from a genelight {adegenet} object
gl.keep.pop Remove all but specified populations from a genelight {adegenet} object
gl.load Retrieves an object in compressed binary format earlier saved using gl.save.
gl.make.recode.ind Create a proforma recode_ind file for reassigning individual (=specimen) names
gl.make.recode.pop Create a proforma recode_pop_table file for reassigning population names
gl.map.interactive Creates an interactive map (based on latlong) from a genlight object
gl.merge.pop Merge two or more populations in a genelight {adegenet} object into one population
gl.nhybrids Create an input file for the program NewHybrids and run it if NewHybrids is installed
gl.outflank Function to identify 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 plot of the results of an ordination generated using gl.pcoa()
gl.pcoa.plot.3d 3D interactive plot of the results of a PCoA ordination
gl.pcoa.scree Produce a plot of eigenvalues, standardized as percentages, derived from a PCoA
gl.percent.freq Generate percentage allele frequencies by locus and population
gl.play.history Replays the history and applies it to a genlight object
gl.plot Plotting genlight object as a smear plot (loci by individuals color coded for scores of 0, 1, 2 and NA)
gl.plot.heatmap Represent a distance matrix as a heatmap
gl.plot.network Represents a distance or dissimilarity matrix as a network
gl.print.history Prints history of a genlight object
gl.propShared Calculate a similarity(distance) matrix for individuals on the proportion of shared alleles
gl.read.csv Read SNP data from a csv file into a genlight object
gl.read.dart Import DarT data into R and conver it to a genlight object
gl.read.silicodart Import 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 Assign a individual metric as pop in a genlight {adegenet} object
gl.recalc.metrics Recalculate locus metrics when individuals or populations are deleted from a genlight {adegenet} object
gl.recode.ind Recode individual (=specimen = sample) labels in a genelight object {adegenet}
gl.recode.pop Recode population assignments in a genlight object {adegenet}
gl.report.bases Summary of base pair frequencies
gl.report.callrate Report summary of Call Rate for loci or individuals
gl.report.diversity Calculate diversity indices for SNPs
gl.report.hamming Calculates the pairwise Hamming distance between DArT trimmed DNA sequences
gl.report.heterozygosity Reports observed and expected heterozygosity by population or by individual from SNP data.
gl.report.hwe Reports departure from Hardy-Weinberg Equilibrium
gl.report.ld Calculates pairwise population based Linkage Disequilibirum across all loci using the specifyied number of cores
gl.report.locmetric Report summary of the slot $other$loc.metrics
gl.report.maf Report minor allele frequency (MAF) for each locus in a SNP dataset
gl.report.monomorphs Report 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 Report private alleles (and fixed alleles) per pair of populations
gl.report.parent.offspring Identify putative parent offspring within a population
gl.report.rdepth Report summary of Read Depth for each locus
gl.report.RepAvg Report summary of RepAvg averaged over both alleles for each locus or reproducibility (repeatability of the scores for fragment presence/absence).
gl.report.reproducibility Report summary of RepAvg (repeatability averaged over both alleles for each locus) or reproducibility (repeatability of the scores for fragment presence/absence).
gl.report.secondaries Report loci containing secondary SNPs in sequence tags
gl.report.sexlinked Identify loci that are sex linked in specimens in a genlight 'adegenet' object
gl.report.taglength Report summary of sequence tag length across loci in a genlight adegenet object
gl.save Save an object in compressed binary format for later rapid retrieval.
gl.set.verbosity Set the default verbosity level
gl.sim.ind Simulates individuals based on the allele frequencies provided via a genlight object.
gl.sim.offspring Simulates a specified number of offsprings based on alleles provided by potential father(s) and mother(s)
gl.stockR Generate a SNP matrix from a genlight {adegenet} object for subsequent use in R package stockR.
gl.subsample.loci Subsample n loci from a genlight object and return as a genlight object
gl.test.heterozygosity Tests the difference in heterozyosity between populations taken pairwise.
gl.tree.nj Output an nj tree to summarize genetic similarity among populations
gl.utils.fdsim Estimate the rate of false positives in a fixed difference analysis
gl.write.csv Write out data from a gl object adegenet to csv file
gl2bayescan Convert a genlight object to format suitable for input to Bayescan
gl2demerelate Create a dataframe suitable for input to package {Demerelate} from a genlight {adegenet} object
gl2fasta Concatenates DArT trimmed sequences and outputs a fastA file.
gl2faststructure Export DArT genlight object {adegenet} to faststructure format (to run faststructure elsewhere)
gl2gds Convert a genlight object to gds format
gl2genalex Convert a genlight object to format suitable for input to genalex
gl2gi Converts a genlight object to genind object
gl2hiphop Converts genlight objects to hiphop format
gl2phylip Create a Phylip input distance matrix from a genlight (SNP) {adegenet} object
gl2plink Converts a genlight object to PLINK file format
gl2related Convert a genlight object to format suitable to be run with Coancestry
gl2sa Convert genlight objects to the format used in the SNPassoc package
gl2shp Convert genlight objects to ESRI shapefiles or kml files
gl2snapp Convert a genlight object to nexus format suitable for phylogenetic analysis by SNAPP (via BEAUti)
gl2structure Converts genlight objects to STRUCTURE formated files
gl2svdquartets Convert a genlight object to nexus format PAUP SVDquartets
gl2treemix Convert a genlight object to a treemix input file

-- I --

is.fixed Test to see if two populations are fixed at a given locus

-- P --

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

-- T --

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_metadata Metadata file. Can be integrated via the dart2genlight function.
testset_pop_recode Recode file to be used with the function.
testset_SNPs_2Row Testfile in DArT format (as provided by DArT)

-- U --

util.outflank OutFLANK: An Fst outlier approach by Mike Whitlock and Katie Lotterhos, University of British Columbia.
util.outflank.MakeDiploidFSTMat Creates OutFLANK input file from individual genotype info.
util.outflank.plotter Plotting functions for Fst distributions after OutFLANK This function takes the output of OutFLANK as input with the OFoutput parameter. It plots a histogram of the FST (by default, the uncorrected FSTs used by OutFLANK) of loci and overlays the inferred null histogram.
utils.dart2genlight Convert DarT to genlight
utils.dist.binary Calculate a distance matrix for individuals defined in an {adegenet} genlight object using binary P/A data (SilicoDArT)
utils.hamming Calculates the Hamming distance between two DArT trimmed DNA sequences
utils.hwe Calculates departure from Hardy-Weinberg Equilibrium. Utility script not meant for end users.
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 This function takes the output of OutFLANK as input with the OFoutput parameter. It plots a histogram of the FST (by default, the uncorrected FSTs used by OutFLANK) of loci and overlays the inferred null histogram.
utils.pa.ind Report number of private alleles possessed by an individual of unknown provenance
utils.prob.hwe Exact SNP test of Hardy-Weinberg Equilibrium
utils.read.dart Import DarT data to R
utils.recalc.avgpic A utility script to recalculate the OneRatioRef, OneRatioSnp, PICRef, PICSnp, and AvgPIC by locus after some 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 the frequency of the heterozygous SNPs by locus after some populations have been deleted
utils.recalc.freqhomref A utility script to recalculate the the frequency of the homozygous reference SNP by locus after some populations have been deleted
utils.recalc.freqhomsnp A utility script to recalculate the the frequency of the homozygous alternate SNP by locus after some populations have been deleted
utils.recalc.maf A utility script to recalculate the 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.