Learn R Programming

⚠️There's a newer version (2.9.9.5) of this package.Take me there.

dartR (version 1.1.11)

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.

Copy Link

Version

Install

install.packages('dartR')

Monthly Downloads

2,264

Version

1.1.11

License

GPL-2

Maintainer

Bernd Gruber

Last Published

February 7th, 2019

Functions in dartR (1.1.11)

A genlight object created via the read.dart functions

gl.costdistances

Calculates cost distances for a given landscape (resistance matrix)

gl.make.recode.ind

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

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

Calculate diversity indices for SNPs

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

gl.make.recode.pop

Create a proforma recode_pop_table file for reassigning population names

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

Recode population assignments in a genelight object {adegenet}

Remove specified individuals from a genelight {adegenet} object

Filter loci on the basis of minor allele frequency (MAF) in a genlight adegenet object

gl.report.bases

Summary of base pair frequencies

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

gl2faststructure

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

Performs and AMOVA using genlight data.

gl.edit.recode.ind

Create or edit a individual (=specimen) names and create an recode_ind file

Assign an individual of unknown provenance to population

gl.dist.heatmap

Represent a distance matrix as a heatmap

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

Convert a genlight object to nexus format PAUP SVDquartets

gl.filter.callrate

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

gl.filter.monomorphs

Remove monomorphic loci, including those with all NAs

Converts a genind object to genlight object

gl.edit.recode.pop

Create or edit a population re-assignment table

Generate a matrix of fixed differences from a genelight or genind object {adegenet}

A very simple function to report observed Heterozygosity

Remove specified populations from a genelight {adegenet} object

Remove specified loci from a genelight {adegenet} object

Calculate a pairwise fst values for populations in a genlight object

gl.filter.cloneid

Filter for CloneID to select only unique SNPs

PCoA ordination (glPca)

Filter function to facilitate analysing of dart data

Isolation by distance

gl.pcoa.plot.3d

3D interactive plot of the results of a PCoA ordination

gl.filter.hamming

Filters loci in a genlight object based on pairwise Hamming distance between sequence tags

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.

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

Filters loci that show significant departure from Hardy-Weinberg Equilibrium

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

Plotting genlight object

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

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

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

gl.genleastcost

Least-cost path analysis based on a friction matrix

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

gl.read.silicodart

Import presence/absence data from SilicoDArT and convert to genind {agegenet} format

gl.report.monomorphs

Report monomorphic loci, including those with all NAs

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

gl.read.dart.2row

Import SNP data from DArT and convert to genlight {agegenet} format (gl)

gl.percent.freq

Generate percentage allele frequencies by locus and population

gl.report.secondaries

Report loci containing secondary SNPs in a genlight {adegenet} object

Estimate the rate of false positives in a fixed difference analysis

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

Converts a genlight object to genind object

Bivariate plot of the results of a PCoA ordination

Write out data from a gl object adegenet to csv file

Convert genlight objects to ESRI shapefiles or kml files

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

A very simple function to report expected Heterozygosity

PCoA ordination of populations

gl.report.callrate

Report summary of Call Rate for loci or individuals

Calculates allele frequency of the first and second allele for each loci #' A very simple function to report allele frequencies

gl.report.hamming

Calculates the pairwise Hamming distance between DArT trimmed DNA sequences

Report minor allele frequency (MAF) for each locus in a genlight adegenet object

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

Convert a genlight object to a treemix input file

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.subsample.loci

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

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

Output an nj tree to summarize genetic similarity among populations

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.

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

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

Calculates the genomic relatedness matrix

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

A simulated genlight object created to run a landscape genetic example

Represents a genomic relatedness matrix as a network

utils.recalc.freqhomref

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

Converts a genlight object to plink file format

utils.recalc.freqhomsnp

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

gl.sim.offspring

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

Converts genlight objects to STRUCTURE formated files

Convert a genlight object to nexus format PAUP SVDquartets

Convert genlight objects to the format used in the SNPassoc package

testset_SNPs_2Row

Testfile in DArT format (as provided by DArT)

A genlight object created via the read.dart functions

utils.recalc.callrate

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

gl.map.interactive

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

testset_metadata

Metadata file. Can be integrated via the dart2genlight function.

testset_pop_recode

Recode file to be used with the function.

util.outflank.MakeDiploidFSTMat

Creates OutFLANK input file from individual genotype info.

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

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

gl.recalc.metrics

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

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

utils.recalc.freqhets

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

gl.report.heterozygosity

Reports hetrozygosity

Reports departure from Hardy-Weinberg Equilibrium

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

Concatenates DArT trimmed sequences and outputs a fastA file.

Exact SNP test of Hardy-Weinberg Equilibrium

Import DarT data to R

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.

Calculates the Hamming distance between two DArT trimmed DNA sequences

utils.recalc.maf

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

Convert DarT to genlight