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dartR (version 1.9.9.1)

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

Description

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, once SNP or related fragment presence/absence data from any source is imported into a genlight object many of the functions can be used. Functions are available for input and output of SNP and silicodart data, for reporting on and filtering on various criteria (e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency). Advanced filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg equilibrium). Other functions are available for visualization after PCoA (Principle Coordinate Analysis), or to facilitate transfer of data between genlight/genind objects and newhybrids, related, phylip, structure, faststructure packages.

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Version

Install

install.packages('dartR')

Monthly Downloads

2,264

Version

1.9.9.1

License

GPL-2

Maintainer

Bernd Gruber

Last Published

May 28th, 2021

Functions in dartR (1.9.9.1)

Collapse a distance matrix by amalgamating populations with pairwise fixed difference count less that a threshold

gl.costdistances

Calculates cost distances for a given landscape (resistance matrix)

gl.edit.recode.pop

Create or edit a population re-assignment table

gl.collapse.recursive

Recursively collapse a distance matrix by amalgamating populations

gl.collapse.pval

Collapse a fixed distance matrix by amalgamating populations for which pairwise fixed differences are not significant

gl.filter.RepAvg

Filter loci in a genlight {adegenet} object based on average repeatability of alleles at a locus

gl.compliance.check

Checks a gl object to see if it complies with dartR expectations, and amends to comply if necessary

gl.filter.hamming

Filters loci based on pairwise Hamming distance between sequence tags

Define a new population in a genlight {adegenet} object on the basis of specified individuals

gl.filter.heterozygosity

Filters individuals with average heterozygosity greater than a specified upper threshold or less than a specified lower threshold.

Remove specified individuals from a genelight {adegenet} object

Remove specified loci from a genelight {adegenet} object

gl.filter.overshoot

Filters loci for which the SNP has been trimmed from the sequence tag along with the adaptor

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.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.

Combines two genlight objects

gl.filter.callrate

Filter loci or specimens in a genlight {adegenet} object based on call rate

gl.filter.sexlinked

Identify loci that are sex linked in specimens in a genlight adegenet object

Calculate a distance matrix for populations defined in an {adegenet} genlight object

Calculate a distance matrix for individuals defined in an {adegenet} genlight object

A very simple function to report observed Heterozygosity

gl.filter.cloneid

Filter for CloneID to select only unique SNPs

gl.filter.taglength

Filter loci in a genlight {adegenet} object based on sequence tag length

Calculates an identity by descent matrix

Remove specified populations from a genelight {adegenet} object

Isolation by distance

gl.pcoa.plot.3d

3D interactive plot of the results of a PCoA ordination

Function to run Hardy-Weinberg tests over each loci and population

Ordination applied to genotypes in a genlight object (PCA), in an fd object, or to a distance matrix (PCoA)

gl.plot.network

Represents a distance or dissimilarity matrix as a network

Merge two or more populations in a genelight {adegenet} object into one population

gl.map.interactive

Creates an interactive map (based on latlong) from a genlight object

gl.percent.freq

Generate percentage allele frequencies by locus and population

gl.play.history

Replays the history and applies it to a genlight object

Filter loci on the basis of minor allele frequency (MAF) in a genlight 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.make.recode.pop

Create a proforma recode_pop_table file for reassigning population names

gl.make.recode.ind

Create a proforma recode_ind file for reassigning individual (=specimen) names

Represents a genomic relatedness matrix as a network

gl.recalc.metrics

Recalculate locus metrics when individuals or populations are deleted from a genlight {adegenet} object

gl.read.silicodart

Import presence/absence data from SilicoDArT to genlight {agegenet} format (ploidy=1)

Import DarT data into R and conver it to a genlight object

gl.print.history

Prints history of a genlight object

gl.filter.monomorphs

Remove monomorphic loci, including those with all NAs

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.report.diversity

Calculate diversity indices for SNPs

Calculate a pairwise fst values for populations in a genlight object

Generate a matrix of fixed differences

Remove all but the specified individuals from a genelight {adegenet} object

gl.report.overshoot

Reports loci for which the SNP has been trimmed from the sequence tag along with the adaptor

Calculate a similarity(distance) matrix for individuals on the proportion of shared alleles

Read SNP data from a csv file into a genlight object

Recode individual (=specimen = sample) labels in a genelight object {adegenet}

Report private alleles (and fixed alleles) per pair of populations

gl.report.rdepth

Report summary of Read Depth for each locus

gl.report.parent.offspring

Identify putative parent offspring within a population

Report minor allele frequency (MAF) for each locus in a SNP dataset

Remove all but specified populations from a genelight {adegenet} object

Remove all but the specified loci from a genelight {adegenet} object

Converts a vcf file into a genlight object

gl.sim.offspring

Simulates a specified number of offsprings based on alleles provided by potential father(s) and mother(s)

Simulates individuals based on the allele frequencies provided via a genlight object.

gl.report.hamming

Calculates the pairwise Hamming distance between DArT trimmed DNA sequences

gl.reassign.pop

Assign a individual metric as pop in a genlight {adegenet} object

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.monomorphs

Report monomorphic loci

Calculates pairwise population based Linkage Disequilibirum across all loci using the specifyied number of cores

Generate a SNP matrix from a genlight {adegenet} object for subsequent use in R package stockR.

gl.report.secondaries

Report loci containing secondary SNPs in sequence tags

gl.report.locmetric

Report summary of the slot $other$loc.metrics

Estimate the rate of false positives in a fixed difference analysis

gl.test.heterozygosity

Tests the difference in heterozyosity between populations taken pairwise.

Output an nj tree to summarize genetic similarity among populations

Converts a genlight object to genind object

Converts genlight objects to hiphop format

A genlight object created via the gl.read.silicodart function

A genlight object created via the gl.read.dart function

gl.subsample.loci

Subsample n loci from a genlight object and return as a genlight object

Convert a genlight object to format suitable to be run with Coancestry

Convert genlight objects to the format used in the SNPassoc package

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

Write out data from a gl object adegenet to csv file

Create a Phylip input distance matrix from a genlight (SNP) {adegenet} object

utils.recalc.freqhomref

A utility script to recalculate the the frequency of the homozygous reference SNP by locus after some populations have been deleted

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.

testset_metadata

Metadata file. Can be integrated via the dart2genlight function.

Converts a genlight object to PLINK file format

OutFLANK: An Fst outlier approach by Mike Whitlock and Katie Lotterhos, University of British Columbia.

utils.recalc.freqhets

A utility script to recalculate the the frequency of the heterozygous SNPs by locus after some populations have been deleted

Calculates the Hamming distance between two DArT trimmed DNA sequences

testset_SNPs_2Row

Testfile in DArT format (as provided by DArT)

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.

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.outflank.MakeDiploidFSTMat

Creates OutFLANK input file from individual genotype info.

Create an input file for the program NewHybrids and run it if NewHybrids is installed

Bivariate plot of the results of an ordination generated using gl.pcoa()

Function to identify loci under selection per population using the outflank method of Whitlock and Lotterhos (2015)

gl.genleastcost

Least-cost path analysis based on a friction matrix

Recode population assignments in a genlight object {adegenet}

Produce a plot of eigenvalues, standardized as percentages, derived from a PCoA

utils.recalc.avgpic

A utility script to recalculate the OneRatioRef, OneRatioSnp, PICRef, PICSnp, and AvgPIC by locus after some populations have been deleted.

OutFLANK: An Fst outlier approach by Mike Whitlock and Katie Lotterhos, University of British Columbia.

utils.recalc.callrate

A utility script to recalculate the callrate by locus after some populations have been deleted

Convert a genlight object to gds format

Retrieves an object in compressed binary format earlier saved using gl.save.

gl.report.RepAvg

Report summary of RepAvg averaged over both alleles for each locus or reproducibility (repeatability of the scores for fragment presence/absence).

Reports departure from Hardy-Weinberg Equilibrium

gl.report.taglength

Report summary of sequence tag length across loci in a genlight adegenet object

gl.report.sexlinked

Identify loci that are sex linked in specimens in a genlight adegenet object

gl.report.heterozygosity

Reports observed and expected heterozygosity by population or by individual from SNP data.

A simulated genlight object created to run a landscape genetic example

gl2faststructure

Export DArT genlight object {adegenet} to faststructure format (to run faststructure elsewhere)

Concatenates DArT trimmed sequences and outputs a fastA file.

utils.dart2genlight

Convert DarT to genlight

Calculates departure from Hardy-Weinberg Equilibrium. Utility script not meant for end users.

Example data set as text file to be imported into a genlight object

Convert a genlight object to format suitable for input to genalex

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.

Report number of private alleles possessed by an individual of unknown provenance

utils.dist.binary

Calculate a distance matrix for individuals defined in an {adegenet} genlight object using binary P/A data (SilicoDArT)

Converts genlight objects to STRUCTURE formated files

utils.recalc.freqhomsnp

A utility script to recalculate the the frequency of the homozygous alternate SNP by locus after some populations have been deleted

Convert a genlight object to nexus format PAUP SVDquartets

gl.report.bases

Summary of base pair frequencies

Plotting genlight object as a smear plot (loci by individuals color coded for scores of 0, 1, 2 and NA)

gl.report.callrate

Report summary of Call Rate for loci or individuals

gl.plot.heatmap

Represent a distance matrix as a heatmap

gl.set.verbosity

Set the default verbosity level

Convert a genlight object to nexus format suitable for phylogenetic analysis by SNAPP (via BEAUti)

Convert genlight objects to ESRI shapefiles or kml files

Create a dataframe suitable for input to package {Demerelate} from a genlight {adegenet} object

Save an object in compressed binary format for later rapid retrieval.

Convert a genlight object to format suitable for input to Bayescan

Convert a genlight object to a treemix input file

utils.recalc.maf

A utility script to recalculate the the minor allele frequency by locus, typically after some populations have been deleted

Exact SNP test of Hardy-Weinberg Equilibrium

testset_pop_recode

Recode file to be used with the function.

utils.read.dart

Import DarT data to R

util.outflank.MakeDiploidFSTMat

Creates OutFLANK input file from individual genotype info.

Test to see if two populations are fixed at a given locus

Assign an individual of unknown provenance to population

Performs and AMOVA using genlight data.

A very simple function to report expected Heterozygosity

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

Converts a genind object to genlight object

Calculates basic statistics for each loci (Hs, Ho, Fis etc.)