Estimates observed Heterozygosity
Eliminates populations as possible source populations for an individual
of unknown provenance, using private alleles
Converts a genind object into a genlight object
A genlight object created via the read.dart functions
Calculates allele frequency of the first and second allele for each loci
A very simple function to report allele frequencies
Estimates expected Heterozygosity
Assign an individual of unknown provenance to population based on PCA
Estimates effective population size using the Linkage Disequilibrium
method based on NeEstimator (V2)
Assign an individual of unknown provenance to population based on Mahalanobis
Distance
Performs AMOVA using genlight data
Checks a genlight object to see if it complies with dartR
expectations and amends it to comply if necessary
Calculates a distance matrix for individuals defined in a genlight object
Comparing simulations against theoretical expectations
Represents a genomic relationship matrix (GRM) as a network
gl.filter.parent.offspring
Filters putative parent offspring within a population
Creates or edits individual (=specimen) names, creates a recode_ind
file and applies the changes to a genlight object
Calculates basic statistics for each loci (Hs, Ho, Fis etc.)
Creates or edits a population re-assignment table
Filters loci based on counts of sequence tags scored at a locus (read
depth)
Aligns nucleotides sequences against those present in a target database
using blastn
Performs Hardy-Weinberg tests over loci and populations
Filters loci that are all NA across individuals and/or populations
with all NA across loci
Calculates cost distances for a given landscape (resistance matrix)
Defines a new population in a genlight object for specified individuals
Checks the current global verbosity
Collapses a distance matrix by amalgamating populations with pairwise
fixed difference count less that a threshold
Removes specified loci from a genlight {adegenet} object
Removes specified populations from a genlight object
Installs all required packages for using all functions
available in dartR
Combines two genlight objects
Filters loci on the basis of minor allele frequency (MAF) in a genlight
adegenet object
Ordination applied to genotypes in a genlight object (PCA), in an fd
object, or to a distance matrix (PCoA)
Filters loci that show significant departure from Hardy-Weinberg
Equilibrium
Filters loci on the basis of numeric information stored in
other$loc.metrics in a genlight {adegenet} object
Calculates a distance matrix for populations with SNP genotypes in a
genlight object
Removes specified individuals from a genlight {adegenet} object
Provides descriptive stats and plots to diagnose potential problems
with Hardy-Weinberg proportions
Filters monomorphic loci, including those with all NAs
Represents a distance matrix as a heatmap
Bivariate or trivariate plot of the results of an ordination generated
using gl.pcoa()
Generates a matrix of fixed differences and associated statistics for
populations taken pairwise
Filters loci that are sex linked
Calculates a pairwise Fst values for populations in a genlight object
Filters loci based on pairwise Hamming distance between sequence tags
Filters loci in a genlight {adegenet} object based on sequence tag
length
Removes all but the specified loci from a genlight {adegenet} object
Filters individuals with average heterozygosity greater than a
specified upper threshold or less than a specified lower threshold
Filters loci that represent secondary SNPs in a genlight object
gl.filter.reproducibility
Filters loci in a genlight {adegenet} object based on average
repeatability of alleles at a locus
Removes all but the specified individuals from a genlight {adegenet}
object
Filters loci or specimens in a genlight {adegenet} object based on
call rate
Performs isolation by distance analysis
Creates an Evanno plot from a STRUCTURE run object
Generates percentage allele frequencies by locus and population
Removes all but the specified populations from a genlight object
Replays the history and applies it to a genlight object
Renames a population in a genlight object
Smear plot of SNP or presence/absence (SilicoDArT) data
Recodes population assignments in a genlight object
Simulates a specified number of offspring based on alleles provided by
potential father(s) and mother(s)
Converts a genlight object into a format suitable for input to genalex
Converts a vcf file into a genlight object
Represents a distance or dissimilarity matrix as a network
Assigns an individual metric as pop in a genlight {adegenet} object
Estimates the rate of false positives in a fixed difference analysis
Converts a genlight object into genepop format (and file)
Reports monomorphic loci
Creates a proforma recode_ind file for reassigning individual
(=specimen) names
Loads an object from compressed binary format produced by gl.save()
Merges two or more populations in a genlight object into one population
Maps a STRUCTURE plot using a genlight object
Prints dartR reports saved in tempdir
Reports summary of Call Rate for loci or individuals
Calculates a similarity (distance) matrix for individuals on the proportion of
shared alleles
Reports summary of base pair frequencies
Prints dartR reports saved in tempdir
Filters loci for which the SNP has been trimmed from the sequence tag
along with the adaptor
Filters loci that contain private (and fixed alleles) between two populations
Converts a genlight object into vcf format
Converts a genlight object to a treemix input file
Testfile in DArT format (as provided by DArT)
Reports private alleles (and fixed alleles) per pair of populations
Selects shapes from the base R shape palette and outputs as a vector
Subsamples n loci from a genlight object and return it as a genlight object
Imputates missing data
Sets the default verbosity level
gl.report.parent.offspring
Identifies putative parent offspring within a population
Tests the difference in heterozygosity between populations taken
pairwise
Imports DArT data into dartR and converts it into a genlight object
Creates an input file for the program NewHybrids and runs it if
NewHybrids is installed
Converts a genlight objects into hiphop format
Imports presence/absence data from SilicoDArT to genlight {agegenet}
format (ploidy=1)
Plots STRUCTURE analysis results (Q-matrix)
Identifies loci under selection per population using the outflank
method of Whitlock and Lotterhos (2015)
Calculates pairwise population based Linkage Disequilibrium across all loci
using the specified number of cores
Calculates pairwise linkage disequilibrium in SNPs mapped to a
reference genome
Reports summary of Read Depth for each locus
Runs Wright-Fisher simulations
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)
Performs least-cost path analysis based on a friction matrix
Calculates an identity by descent matrix
Metadata file. Can be integrated via the dart2genlight function.
Creates a proforma recode_pop_table file for reassigning population
names
Conducts jackknife resampling using a genlight object
Reports loci for which the SNP has been trimmed from the sequence tag
along with the adaptor
Prints history of a genlight object
A utility script to calculate the number of variant and invariant sites by
locus
Creates a Phylip input distance matrix from a genlight (SNP) {adegenet}
object
Calculates diversity indexes for SNPs
Calculates the pairwise Hamming distance between DArT trimmed DNA
sequences
Reports observed, expected and unbiased heterozygosities and FIS
(inbreeding coefficient) by population or by individual from SNP data
Saves an object in compressed binary format for later rapid retrieval
A utility script to recalculate the frequency of the homozygous alternate
SNP by locus after some populations have been deleted
Creates the reference table for running gl.sim.WF.run
Selects colors from one of several palettes and output as a vector
Randomly changes the allocation of 0's and 2's in a genlight object
Recalculates locus metrics when individuals or populations are deleted from a
genlight {adegenet} object
Creates an interactive map (based on latlon) from a genlight object
A utility script to recalculate the minor allele frequency by locus,
typically after some populations have been deleted
Reads SNP data from a csv file into a genlight object
Writes out data from a genlight object to csv file
Outputs an nj tree to summarize genetic similarity among populations
Converts a genlight object to geno format from package LEA
Converts a genlight object to genind object
Simulates individuals based on the allele frequencies provided via a genlight
object.
Recodes individual (=specimen = sample) labels in a genlight object
Converts a genlight object to nexus format PAUP SVDquartets
Calculates expected mean expected heterozygosity per population
Converts a genlight object to STRUCTURE formated files
Calculates the Hamming distance between two DArT trimmed DNA sequences
Reports summary of the slot $other$loc.metrics
Reports minor allele frequency (MAF) for each locus in a SNP dataset
Reports loci containing secondary SNPs in sequence tags and calculates
number of invariant sites
Identifies loci that are sex linked
Shiny app for the input of the reference table for the simulations
A genlight object created via the gl.read.dart function
Shiny app for the input of the simulations variables
Converts a genlight object into faststructure format (to run faststructure
elsewhere)
Simulates mutations within a genlight object
A genlight object created via the gl.read.silicodart function
A utility script to recalculate the frequency of the heterozygous SNPs by
locus after some populations have been deleted
Reports departure from Hardy-Weinberg proportions
A utility script to recalculate the frequency of the homozygous reference
SNP by locus after some populations have been deleted
Setting up the package
Converts a genlight object into a format suitable for input to Bayescan
A utility script to flag the start of a script
utils.structure.genind2gtypes
structure util functions
Calculates a distance matrix for individuals defined in a dartR
genlight object using SNP data (DArTseq)
Converts a genlight object into gds format
Creates a dataframe suitable for input to package {Demerelate} from a
genlight {adegenet} object
Converts a genlight object into PLINK format
Utility function to run strcture
Converts a genlight object to format suitable to be run with Coancestry
Recode file to be used with the function.
dartR theme
Runs a STRUCTURE analysis using a genlight object
Reports summary of sequence tag length across loci
Creates a dispersal file as input for the function gl.sim.WF.run
Converts genlight objects to the format used in the SNPassoc package
Concatenates DArT trimmed sequences and outputs a FASTA file
Simulates emigration between populations
Converts a genlight object to ESRI shapefiles or kml files
Converts a genlight object into eigenstrat format
Tests if two populations are fixed at a given locus
Converts a genlight object to nexus format suitable for phylogenetic analysis
by SNAPP (via BEAUti)
Example data set as text file to be imported into a genlight object
Converts DarT to genlight
Calculates a distance matrix for individuals defined in a dartR
genlight object using binary P/A data (SilicoDArT)
utils.outflank.MakeDiploidFSTMat
Creates OutFLANK input file from individual genotype info.
Converts a genlight object into a sfs input file
OutFLANK: An Fst outlier approach by Mike Whitlock and Katie Lotterhos,
University of British Columbia.
A simulated genlight object created to run a landscape genetic example
Calculates mean observed heterozygosity, mean expected heterozygosity and Fis
per locus, per population and Fst across all populations
A utility script to recalculate the callrate by locus after some populations
have been deleted
A utility script to recalculate the OneRatioRef, OneRatioSnp, PICRef, PICSnp,
and AvgPIC by locus after some individuals or populations have been deleted.
A genlight object created via the gl.read.dart function
Utility function to check the class of an object passed to a function
Imports DarT data to R
Plotting functions for Fst distributions after OutFLANK
A utility script to reset to FALSE (or TRUE) the locus metric flags after
some individuals or populations have been deleted.
Util function for evanno plots