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


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Documentation for package ‘dartR’ version 1.1.11

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B D G I P R T U

-- B --

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

-- D --

dart2genlight Convert DarT to genlight

-- 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
gl.collapse.pval Collapse a fixed distance matrix by amalgamating populations for which fixed differences are not significant
gl.collapse.recursive Recursively collapse a distance matrix by amalgamating populations
gl.costdistances Calculates cost distances for a given landscape (resistance matrix)
gl.define.pop Define a new population in a genelight {adegenet} object on the basis of specified individuals
gl.dist.heatmap Represent a distance matrix as a heatmap
gl.dist.pop Calculate a distance matrix for populations defined in an {adegenet} genlight object
gl.diversity Calculate diversity indices for SNPs
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 and create an recode_ind file
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 in a genlight object based on pairwise Hamming distance between sequence tags
gl.filter.hwe Filters loci that show significant departure from Hardy-Weinberg Equilibrium
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.repavg 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.fixed.diff Generate a matrix of fixed differences from a genelight or genind object {adegenet}
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 the genomic relatedness matrix
gl.grm.network Represents a genomic relatedness matrix as a network
gl.Ho A very simple function to report observed Heterozygosity
gl.Hs A very simple function to report expected Heterozygosity
gl.hwe.pop Filter function to facilitate analysing of dart data
gl.ibd Isolation by distance
gl.keep.ind Remove all but the specified individuals from a genelight {adegenet} object
gl.keep.pop Remove all but specified populations from a genelight {adegenet} object
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 PCoA ordination (glPca)
gl.pcoa.plot Bivariate plot of the results of a PCoA ordination
gl.pcoa.plot.3d 3D interactive plot of the results of a PCoA ordination
gl.pcoa.pop PCoA ordination of populations
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.plot Plotting genlight object
gl.read.dart Import DarT data into R and conver it to a genlight object
gl.read.dart.2row Import SNP data from DArT and convert to genlight {agegenet} format (gl)
gl.read.silicodart Import presence/absence data from SilicoDArT and convert to genind {agegenet} format
gl.recalc.metrics Recalculate locus metrics when individuals or populations are deleted from a genlight {adegenet} object
gl.recode.ind Recode individual (=specimen) labels in a genelight or genind object {adegenet}
gl.recode.pop Recode population assignments in a genelight object {adegenet}
gl.report.bases Summary of base pair frequencies
gl.report.callrate Report summary of Call Rate for loci or individuals
gl.report.hamming Calculates the pairwise Hamming distance between DArT trimmed DNA sequences
gl.report.heterozygosity Reports hetrozygosity
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.maf Report minor allele frequency (MAF) for each locus in a genlight adegenet object
gl.report.monomorphs Report monomorphic loci, including those with all NAs
gl.report.pa Report number of private alleles possessed by an individual of unknown provenance
gl.report.pa.pop Report private alleles (and fixed alleles) per pair of populations
gl.report.repavg Report summary of RepAvg, reproducibility averaged over both alleles for each locus in a genlight adegenet object
gl.report.secondaries Report loci containing secondary SNPs in a genlight {adegenet} object
gl.sexlinkage Identify loci that are sex linked in specimens in a genlight {adegenet} object
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.subsample.loci Subsample n loci from a genlight object and return as a genlight object
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
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 nexus format PAUP SVDquartets
gl2gi Converts a genlight object to genind object
gl2phylip Create a Phylip input distance matrix from a genlight (SNP) or genind (SilicoDarT) {adegenet} object
gl2plink Converts a genlight object to plink file format
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
prob.hwe Exact SNP test of Hardy-Weinberg Equilibrium

-- R --

read.dart Import DarT data to R

-- T --

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