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

## Documentation for package ‘dartR’ version 1.1.11

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

## Help Pages

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