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

## Documentation for package ‘dartR’ version 1.9.6

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

## Help Pages

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.