Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis
A genlight object created via the read.dart functions
adjust cbind for dartR
Converts a genind object into a genlight object
Calculates allele frequency of the first and second allele for each lo...
Generates percentage allele frequencies by locus and population
Performs AMOVA using genlight data
Population assignment using grm
Assign an individual of unknown provenance to population based on Maha...
Eliminates populations as possible source populations for an individua...
Assign an individual of unknown provenance to population based on PCA
Calculates basic statistics for each loci (Hs, Ho, Fis etc.)
Aligns nucleotides sequences against those present in a target databas...
Checks the current global verbosity
Checks the global working directory
Collapses a distance matrix by amalgamating populations with pairwise ...
This is a helper function that supports the creation of color palettes...
Checks a genlight object to see if it complies with dartR expectations...
Calculates cost distances for a given landscape (resistance matrix)
Defines a new population in a genlight object for specified individual...
Provides descriptive stats and plots to diagnose potential problems wi...
Comparing simulations against theoretical expectations
Calculates a distance matrix for individuals defined in a genlight obj...
Calculates a distance matrix for populations with SNP genotypes in a g...
Removes specified individuals from a dartR genlight object
Removes specified loci from a dartR genlight object
Removes specified populations from a dartR genlight object
Creates or edits individual (=specimen) names, creates a recode_ind fi...
Creates or edits and applies a population re-assignment table
Creates an Evanno plot from a STRUCTURE run object
Estimates the rate of false positives in a fixed difference analysis
Filters loci that are all NA across individuals and/or populations wit...
Filters loci or specimens in a genlight {adegenet} object based on cal...
Filters loci based on pairwise Hamming distance between sequence tags
Filters individuals with average heterozygosity greater than a specifi...
Filters loci that show significant departure from Hardy-Weinberg Equil...
Filters loci on the basis of numeric information stored in other$loc.m...
Filters loci on the basis of minor allele frequency (MAF) in a genligh...
Filters monomorphic loci, including those with all NAs
Filters loci for which the SNP has been trimmed from the sequence tag ...
Filters loci that contain private (and fixed alleles) between two popu...
Filters putative parent offspring within a population
Filters loci based on counts of sequence tags scored at a locus (read ...
Filters loci in a genlight {adegenet} object based on average repeatab...
Filters loci that represent secondary SNPs in a genlight object
Filters loci that are sex linked
Filters loci in a genlight {adegenet} object based on sequence tag len...
Generates a matrix of fixed differences and associated statistics for ...
Calculates a pairwise Fst values for populations in a genlight object
Performs least-cost path analysis based on a friction matrix
Represents a genomic relationship matrix (GRM) as a network
Calculates an identity by descent matrix
Estimates expected Heterozygosity
Estimates observed Heterozygosity
Performs Hardy-Weinberg tests over loci and populations
Performs isolation by distance analysis
Imputates missing data
Installs all required packages for using all functions available in da...
Combines two genlight objects
Removes all but the specified individuals from a dartR genlight object
Removes all but the specified loci from a genlight object
Removes all but the specified populations from a dartR genlight object
Plots linkage disequilibrium against distance by population disequilib...
Visualize patterns of linkage disequilibrium and identification of hap...
Estimates effective population size using the Linkage Disequilibrium m...
Prints dartR reports saved in tempdir
Loads an object from compressed binary format produced by gl.save()
Creates a proforma recode_ind file for reassigning individual (=specim...
Creates a proforma recode_pop_table file for reassigning population na...
Creates an interactive map (based on latlon) from a genlight object
Maps a STRUCTURE plot using a genlight object
Merges two or more populations in a genlight object into one populatio...
Creates an input file for the program NewHybrids and runs it if NewHyb...
Identifies loci under selection per population using the outflank meth...
Bivariate or trivariate plot of the results of an ordination generated...
Ordination applied to genotypes in a genlight object (PCA), in an fd o...
Generates percentage allele frequencies by locus and population
Replays the history and applies it to a genlight object
Plots fastStructure analysis results (Q-matrix)
Represents a distance matrix as a heatmap
Represents a distance or dissimilarity matrix as a network
Plots STRUCTURE analysis results (Q-matrix)
Prints history of a genlight object
Prints dartR reports saved in tempdir
Calculates a similarity (distance) matrix for individuals on the propo...
Randomly changes the allocation of 0's and 2's in a genlight object
Reads SNP data from a csv file into a genlight object
Imports DArT data into dartR and converts it into a dartR genlight obj...
Reads FASTA files and converts them to genlight object
Imports presence/absence data from SilicoDArT to genlight {agegenet} f...
Converts a vcf file into a genlight object
Assigns an individual metric as pop in a genlight {adegenet} object
Recalculates locus metrics when individuals or populations are deleted...
Recodes individual (=specimen = sample) labels in a genlight object
Recodes population assignments in a genlight object
Renames a population in a genlight object
Reports summary of base pair frequencies
Reports summary of Call Rate for loci or individuals
Calculates diversity indexes for SNPs
Reports various statistics of genetic differentiation between populati...
Calculates the pairwise Hamming distance between DArT trimmed DNA sequ...
Reports observed, expected and unbiased heterozygosities and FIS (inbr...
Reports departure from Hardy-Weinberg proportions
Calculates pairwise linkage disequilibrium by population
Reports summary of the slot loc.metrics
Reports minor allele frequency (MAF) for each locus in a SNP dataset
Reports monomorphic loci
Reports loci for which the SNP has been trimmed from the sequence tag ...
Reports private alleles (and fixed alleles) per pair of populations
Identifies putative parent offspring within a population
Reports summary of Read Depth for each locus
Identify replicated individuals
Reports summary of RepAvg (repeatability averaged over both alleles fo...
Reports loci containing secondary SNPs in sequence tags and calculates...
Identifies loci that are sex linked
Reports summary of sequence tag length across loci
Runs a faststructure analysis using a genlight object
Runs a STRUCTURE analysis using a genlight object
Samples individuals from populations
Saves an object in compressed binary format for later rapid retrieval
Selects colors from one of several palettes and output as a vector
Selects shapes from the base R shape palette and outputs as a vector
Sets the default verbosity level
Creates a site frequency spectrum based on a dartR or genlight object
Creates a dispersal file as input for the function gl.sim.WF.run
Simulates emigration between populations
Simulates individuals based on the allele frequencies provided via a g...
Simulates mutations within a genlight object
Simulates a specified number of offspring based on alleles provided by...
Runs Wright-Fisher simulations
Creates the reference table for running gl.sim.WF.run
Smear plot of SNP or presence/absence (SilicoDArT) data
re-sorts genlight objects
Spatial autocorrelation following Smouse and Peakall 1999
Subsamples n loci from a genlight object and return it as a genlight o...
Tests the difference in heterozygosity between populations taken pairw...
Outputs an nj tree to summarize genetic similarity among populations
Writes out data from a genlight object to csv file
Converts a genlight object into a format suitable for input to Bayesca...
Converts a genlight object into a format suitable for input to the BPP...
Convert a genlight object to a dartR object
Creates a dataframe suitable for input to package {Demerelate} from a ...
Converts a genlight object into eigenstrat format
Concatenates DArT trimmed sequences and outputs a FASTA file
Converts a genlight object into faststructure format (to run faststruc...
Converts a genlight object into gds format
Converts a genlight object into a format suitable for input to genalex
Converts a genlight object into genepop format (and file)
Converts a genlight object to geno format from package LEA
Converts a genlight object to genind object
Converts a genlight objects into hiphop format
Creates a Phylip input distance matrix from a genlight (SNP) {adegenet...
Converts a genlight object into PLINK format
Converts a genlight object to format suitable to be run with Coancestr...
Converts genlight objects to the format used in the SNPassoc package
Converts a genlight object into a sfs input file
Converts a genlight object to ESRI shapefiles or kml files
Converts a genlight object to nexus format suitable for phylogenetic a...
Converts a genlight object to STRUCTURE formatted files
Converts a genlight object to nexus format PAUP SVDquartets
Converts a genlight object to a treemix input file
Converts a genlight object into vcf format
Shiny app for the input of the reference table for the simulations
Shiny app for the input of the simulations variables
Tests if two populations are fixed at a given locus
Example data set as text file to be imported into a genlight object
adjust rbind for dartR
indexing dartR objects correctly...
Metadata file. Can be integrated via the dart2genlight function.
Recode file to be used with the function.
Testfile in DArT format (as provided by DArT)
dartR theme
Population assignment probabilities
Population assignment probabilities
Population assignment probabilities
Population assignment probabilities
Calculates mean observed heterozygosity, mean expected heterozygosity ...
Utility function to check the class of an object passed to a function
Functions from package starmie for merging Q matrices from Structure r...
Converts DarT to genlight.
Calculates a distance matrix for individuals defined in a dartR genlig...
Calculates a distance matrix for individuals defined in a dartR genlig...
A utility script to flag the start of a script
Calculates the Hamming distance between two DArT trimmed DNA sequences
Calculates expected mean expected heterozygosity per population
Conducts jackknife resampling using a genlight object
A utility script to calculate the number of variant and invariant site...
Creates OutFLANK input file from individual genotype info.
Plotting functions for Fst distributions after OutFLANK
OutFLANK: An Fst outlier approach by Mike Whitlock and Katie Lotterhos...
An internal function to save a ggplot object to disk in RDS binary for...
utility function to read in DArT data
A utility script to recalculate the OneRatioRef, OneRatioSnp, PICRef, ...
A utility script to recalculate the callrate by locus after some popul...
A utility script to recalculate the frequency of the heterozygous SNPs...
A utility script to recalculate the frequency of the homozygous refere...
A utility script to recalculate the frequency of the homozygous altern...
A utility script to recalculate the minor allele frequency by locus, t...
A utility script to reset to FALSE (or TRUE) the locus metric flags af...
Spatial autocorrelation coefficient calculations
Util function for evanno plots
structure util functions
Utility function to run Structure
Setting up the package
Functions are provided that facilitate the import and analysis of 'SNP' (single nucleotide polymorphism) and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT' (Diversity Arrays Technology), however, data from other sequencing platforms can be used once 'SNP' or related fragment presence/absence data from any source is imported. Genetic datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for a very compact storage of data and metadata. Functions are available for importing and exporting of 'SNP' and 'silicodart' data, for reporting on and filtering on various criteria (e.g. 'CallRate', heterozygosity, reproducibility, maximum allele frequency). Additional functions are available for visualization (e.g. Principle Coordinate Analysis) and creating a spatial representation using maps. 'dartR' supports also the analysis of 3rd party software package such as 'newhybrid', 'structure', 'NeEstimator' and 'blast'. Since version 2.0.3 we also implemented simulation functions, that allow to forward simulate 'SNP' dynamics under different population and evolutionary dynamics. Comprehensive tutorials and support can be found at our 'github' repository: github.com/green-striped-gecko/dartR/. If you want to cite 'dartR', you find the information by typing citation('dartR') in the console.
Useful links