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dartR (version 0.80)

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 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. Other functions are available for visualization after PCoA, or to facilitate transfer of data between genlight/genind objects and newhybrids, related, phylip packages etc.

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Version

Install

install.packages('dartR')

Monthly Downloads

4,205

Version

0.80

License

GPL-2

Maintainer

Bernd Gruber

Last Published

June 23rd, 2017

Functions in dartR (0.80)

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

gl.edit.recode.ind

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

Filter function to facilitate analysing of dart data

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

Collapse a distance matrix by amalgamating populations

gl.collapse.recursive

Recursively collapse a distance matrix by amalgamating populations

Convert DarT to genlight

Filter function to facilitate analysing of dart data [deprecated use explicit filter functions gl.filter...]

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

Converts a genind object to genlight object

gl.filter.cloneid

Filter for CloneID to select only unique SNPs

Filter duplicated loci in a genlight {adegenet} object

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

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.

Bivariate plot of the results of a PCoA ordination

PCoA ordination of populations

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

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

gl.make.recode.ind

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

gl.make.recode.pop

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

gl.report.callrate

Report summary of Call Rate for loci or individuals

Report duplicated loci in a genlight {adegenet} object

gl2faststructure

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

Convert a genlight object to gds format SNPRelate

A genlight object created via the read.dart functions

testset_SNPs_2Row

Testfile in DArT format (as provided by DArT)

gl.filter.hamming

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

Filters loci that show significant departure from Hardy-Weinberg Equilibrium

PCoA ordination (glPca)

gl.pcoa.plot.3d

3D interactive plot of the results of a PCoA ordination

gl.read.silicodart

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

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

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

Concatenates DArT trimmed sequences and outputs a fastA file.

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

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

Reports departure from Hardy-Weinberg Equilibrium

gl.report.monomorphs

Report monomorphic loci, including those with all NAs

gl.report.repavg

Report summary of RepAvg, reproducibility averaged over both alleles for each locus in a genlight adegenet object

gl.read.dart.arthur

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

gl.report.hamming

Calculates the pairwise Hamming distance between DArT trimmed DNA sequences

gl.report.heterozygosity

Reports hetrozygosity

Output an nj tree to summarize genetic similarity among populations

Write out data from a gl object adegenet to csv file

Exact SNP test of Hardy-Weinberg Equilibrium

Import DarT data to R

gl.subsample.loci

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

Calculates the Hamming distance between two DArT trimmed DNA sequences

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

gl.filter.monomorphs

Remove monomorphic loci, including those with all NAs

gl.filter.repavg

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

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

gl.percent.freq

Generate percentage allele frequencies by locus and population

Recode population assignments in a genelight or genind object {adegenet}

gl.report.bases

Summary of base pair frequencies

Converts a genlight object to genind object

Create an input file for the program NewHybrids

testset_metadata

Metadata file. Can be integrated via the dart2genlight function.

testset_pop_recode

Recode file to be used with the function.