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

## Documentation for package ‘dartR’ version 2.0.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

B G I P T U Z

## -- B --

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

## -- G --

gi2gl | Converts a genind object into a 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 AMOVA using genlight data
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.locmetric | Filters loci on the basis of numeric information stored in other$loc.metrics in a genlight {adegenet} object
gl.filter.locmetrics | Filters loci on the basis of numeric information stored in other$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.He | Estimates expected Heterozygosity
gl.Ho | Estimates observed Heterozygosity
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.LDNe | Estimates effective population size using the Linkage Disequilibrium method based on NeEstimator (V2)
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 a STRUCTURE analysis using a genlight object
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.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 in SNPs mapped to a reference genome
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.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.sim.WF.run | Runs Wright-Fisher simulations
gl.sim.WF.table | Creates the reference table for running gl.sim.WF.run
gl.smearplot | Smear plot of SNP or presence/absence (SilicoDArT) data
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
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

## -- I --

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

## -- P --

platy | Example data set as text file to be imported into a genlight object
platypus.gl | A genlight object created via the gl.read.dart function
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)
theme_dartR | dartR theme

## -- U --

utils.basic.stats

Calculates mean observed heterozygosity, mean expected heterozygosity and Fis per locus, per population and Fst across all populations This is a re-implementation of 'hierfstat::basics.stats' specifically for genlight objects. Formula (and hence results) match exactly the original version of 'hierfstat::basics.stats' (although Dstp and Fstp are not currently computed) but it is much faster.

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 | 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
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.structure.evanno | Util function for evanno plots
utils.structure.genind2gtypes | structure util functions
utils.structure.run | Utility function to run strcture

## -- Z --

zzz | Setting up the package