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dartR.base (version 0.98)

Analysing 'SNP' and 'Silicodart' Data - Basic Functions

Description

Facilitates 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.base' is the 'base' package of the 'dartRverse' suits of packages. To install the other packages, we recommend to install the 'dartRverse' package, that supports the installation of all packages in the 'dartRverse'. If you want to cite 'dartR', you find the information by typing citation('dartR.base') in the console.

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Version

Install

install.packages('dartR.base')

Monthly Downloads

1,133

Version

0.98

License

GPL (>= 3)

Maintainer

Bernd Gruber

Last Published

September 19th, 2024

Functions in dartR.base (0.98)

gl.diagnostics.hwe

Provides descriptive stats and plots to diagnose potential problems with Hardy-Weinberg proportions @family matched report
gl.filter.ld

Filters loci based on linkage disequilibrium (LD)
gl.filter.locmetric

Filters loci on the basis of numeric information stored in other$loc.metrics in a genlight {adegenet} object
gl.dist.ind

Calculates a distance matrix for individuals defined in a genlight object
gl.filter.callrate

Filters loci or specimens in a genlight {adegenet} object based on call rate
gl.filter.allna

Filters loci that are all NA across individuals and/or populations with all NA across loci
gl.dist.phylo

Generates a distance matrix taking into account a substitution model
gl.dist.pop

Calculates a distance matrix for populations with SNP genotypes in a genlight object
gl.fdsim

Estimates the rate of false positives in a fixed difference analysis
gl.edit.recode.pop

Creates or edits and applies a population re-assignment table
gl.define.pop

Defines a new population in a genlight object for specified individuals
gl.compliance.check

Checks a genlight object to see if it complies with dartR expectations and amends it to comply if necessary @family environment
gl.filter.pa

Filters loci that contain private (and fixed alleles) between two populations
gl.filter.overshoot

Filters loci for which the SNP has been trimmed from the sequence tag along with the adaptor
gl.drop.ind

Removes specified individuals from a dartR genlight object
gl.filter.factorloadings

Filters loci based on factor loadings for a PCA or PCoA
gl.fixed.diff

Generates a matrix of fixed differences and associated statistics for populations taken pairwise
gl.fst.pop

Calculates a pairwise Fst values for populations in a genlight object This script calculates pairwise Fst values based on the implementation in the StAMPP package (?stamppFst). It allows to run bootstrap to estimate probability of Fst values to be different from zero. For detailed information please check the help pages (?stamppFst).
gl.drop.loc

Removes specified loci from a dartR genlight object
gl.filter.hamming

Filters loci based on pairwise Hamming distance between sequence tags
gl.filter.hwe

Filters loci that show significant departure from Hardy-Weinberg Equilibrium @family matched filter
gl.filter.heterozygosity

Filters individuals with average heterozygosity greater than a specified upper threshold or less than a specified lower threshold @family matched filter
gl.drop.pop

Removes specified populations from a dartR genlight object
gl.mahal.assign

Assigns individuals to populations with an associated probability
gl.load

Loads an object from compressed binary format produced by gl.save()
gl.edit.recode.ind

Creates or edits individual (=specimen) names, creates a recode_ind file and applies the changes to a genlight object @family data manipulation
gl.filter.secondaries

Filters loci that represent secondary SNPs in a genlight object
gl.filter.taglength

Filters loci in a genlight {adegenet} object based on sequence tag length @family matched filter
gl.randomize.snps

Randomly changes the allocation of 0's and 2's in a genlight object
gl.make.recode.pop

Creates a proforma recode_pop_table file for reassigning population names @family data manipulation
gl.make.recode.ind

Creates a proforma recode_ind file for reassigning individual (=specimen) names
gl.prop.shared

Calculates a similarity (distance) matrix for individuals on the proportion of shared alleles @family distance
gl.filter.rdepth

Filters loci based on counts of sequence tags scored at a locus (read depth) @family matched filter
gl.hwe.pop

Performs Hardy-Weinberg tests over loci and populations
gl.impute

Imputes missing data
gl.pcoa.plot

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

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

Filters monomorphic loci, including those with all NAs
gl.filter.maf

Filters loci on the basis of minor allele frequency (MAF) or minor allele count (MAC)
gl.filter.reproducibility

Filters loci in a genlight {adegenet} object based on average repeatability of alleles at a locus @family matched filter
gl.plot.heatmap

Represents a distance matrix as a heatmap
gl.read.PLINK

Reads PLINK data file into a genlight object
gl.read.csv

Reads SNP data from a csv file into a genlight object
gl.read.vcf

Converts a vcf file into a genlight object
gl.read.silicodart

Imports presence/absence data from SilicoDArT to genlight {agegenet} format (ploidy=1)
gl.print.history

Prints history of a genlight object
gl.read.fasta

Reads FASTA files and converts them to genlight object
gl.read.dart

Imports DArT data into dartR and converts it into a dartR genlight object
gl.report.bases

Reports summary of base pair frequencies
gl.report.basics

Basic statistics for a genlight object
gl.rename.pop

Renames a population in a genlight object
gl.report.ld.map

Calculates pairwise linkage disequilibrium by population
gl.keep.loc

Removes all but the specified loci from a genlight object
gl.report.fstat

Reports various statistics of genetic differentiation between populations with confidence intervals
gl.report.locmetric

Reports summary of the slot $other$loc.metrics
gl.report.factorloadings

Reports factor loadings for a PCA or PCoA
gl.report.allna

Reports loci that are all NA across individuals and/or populations with all NA across loci
gl.keep.pop

Removes all but the specified populations from a dartR genlight object
gl.report.ld

Calculates pairwise population based Linkage Disequilibrium across all loci using the specified number of cores @family matched report
gl.join

Combines two dartR genlight objects
gl.report.hwe

Reports departure from Hardy-Weinberg proportions
gl.write.csv

Writes out data from a genlight object to csv file
gl.report.callrate

Reports summary of Call Rate for loci or individuals
gl.select.shapes

Selects shapes from the base R shape palette and outputs as a vector
gl.select.colors

Selects colors from one of several palettes and outputs as a vector
gl.report.diversity

Calculates diversity indexes for SNPs
gl.report.polyploid_heterozygosity

Reports observed, expected and unbiased heterozygosities and FIS (inbreeding coefficient) by population or by individual from SNP data
gl.report.rdepth

Reports summary of Read Depth for each locus
gl.subsample.loci

Subsamples n loci from a genlight object and return it as a genlight object
gl.test.heterozygosity

Tests the difference in heterozygosity between populations taken pairwise
gl.recode.ind

Recodes individual (=specimen = sample) labels in a genlight object
gl.report.secondaries

Reports loci containing secondary SNPs in sequence tags and calculates number of invariant sites
gl.tree.fitch

Generates a distance phylogeny
gl.tree.nj

Outputs a tree to summarize genetic similarity among populations (e.g. phenogram)
gl.report.taglength

Reports summary of sequence tag length across loci
gl.keep.ind

Removes all but the specified individuals from a dartR genlight object
gl.map.interactive

Creates an interactive map (based on latlon) from a genlight object
gl2gds

Converts a genlight object into gds format
gl2bayesAss

Converts a genlight object into bayesAss (BA3) input format
gl2genalex

Converts a genlight object into a format suitable for input to genalex
gl.report.overshoot

Reports loci for which the SNP has been trimmed from the sequence tag along with the adaptor
gl.merge.pop

Merges two or more populations in a dartR genlight object into one population
gl.report.pa

Reports private alleles (and fixed alleles) per pair of populations
gl.recode.pop

Recodes population assignments in a genlight object
gl2related

Converts a genlight object to format suitable to be run with Coancestry
gl2sa

Converts genlight objects to the format used in the SNPassoc package
gl2genepop

Converts a genlight object into genepop format (and file)
gl2geno

Converts a genlight object to geno format from package LEA
gl.reassign.pop

Assigns an individual metric as pop in a genlight {adegenet} object
theme_dartR

Default theme for dartR plots
[,dartR,ANY,ANY,ANY-method

indexing dartR objects correctly...
gl2snapper

Converts a genlight object to nexus format suitable for phylogenetic analysis by Snapper (via BEAUti) @family linker
gl2structure

Converts a genlight object to STRUCTURE formatted files
gl.report.heterozygosity

Reports observed, expected and unbiased heterozygosities and FIS (inbreeding coefficient) by population or by individual from SNP data
gl.report.hamming

Calculates the pairwise Hamming distance between DArT trimmed DNA sequences
utils.plink.run

Runs PLINK from within R
utils.flag.start

A utility script to flag the start of a script
gl2fasta

Concatenates DArT trimmed sequences and outputs a FASTA file
utils.dist.ind.snp

Calculates a distance matrix for individuals defined in a genlight object using SNP data (DArTseq)
gl2faststructure

Converts a genlight object into faststructure format (to run faststructure elsewhere)
utils.plot.save

An internal function to save a ggplot object to disk in RDS binary format
gl.recalc.metrics

Recalculates locus metrics when individuals or populations are deleted from a genlight {adegenet} object @family environment
gl.report.replicates

Identify replicated individuals
utils.recalc.callrate

A utility script to recalculate the callrate by locus after some populations have been deleted
utils.basic.stats

Calculates mean observed heterozygosity, mean expected heterozygosity and FIS per locus, per population and various population differentiation measures @family utilities
utils.recalc.freqhomsnp

A utility function to recalculate the frequency of the homozygous alternate SNP by locus after some populations have been deleted
utils.check.datatype

Utility function to check the class of an object passed to a function
utils.read.fasta

An internal script to read a fastA file into a genlight object
utils.recalc.freqhomref

#' An internal utility function to recalculate the frequency of the homozygous reference SNP by locus after some populations have been deleted
utils.read.dart

Utility to import DarT data to R
gl.report.monomorphs

Reports monomorphic loci
gl.report.maf

Reports minor allele frequency (MAF) for each locus in a SNP dataset
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)
gl.sim.cross

Generates random crosses between fathers and mothers
gl.sim.genotypes

Generate random genotypes
gl.save

Saves an object in compressed binary format for later rapid retrieval
gl.sample

Samples individuals from populations
zzz

Setting up the package Setting theme, colors and verbosity
gl2bayescan

Converts a genlight object into a format suitable for input to Bayescan
gl.set.verbosity

Sets the default verbosity level
gl.subsample.ind

Subsample individuals from a genlight object
gl2bpp

Converts a genlight object into a format suitable for input to the BPP program
utils.recalc.freqhets

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

Sets the default working directory
gl2phylip

Creates a Phylip input distance matrix from a genlight (SNP) {adegenet} object
gl2plink

Converts a genlight object into PLINK format
gl.subsample.loc

Subsample loci from a genlight object
utils.dist.binary

Calculates a distance matrix for individuals defined in a dartR genlight object using binary P/A data (SilicoDArT)
utils.impute

An internal script [Custodian to provide a title]
utils.dart2genlight

An internal function to converts DarT to genlight.
gl2gi

Converts a genind object into a genlight object
gl2hiphop

Converts a genlight objects into hiphop format
utils.is.fixed

An internal function to tests if two populations are fixed at a given locus
utils.reset.flags

#' An internal utility function to reset to FALSE (or TRUE) the locus metric flags after some individuals or populations have been deleted.
utils.recalc.maf

A utility function to recalculate the minor allele frequency by locus, typically after some populations have been deleted
utils.read.ped

An internal script [Custodian to provide a title]
gl.smearplot

Smear plot
gl2vcf

Converts a genlight object into vcf format
rbind.dartR

adjust rbind for dartR
gl.sort

re-sorts genlight objects
gl2demerelate

Creates a dataframe suitable for input to package {Demerelate} from a genlight {adegenet} object
utils.hamming

Calculates the Hamming distance between two DArT trimmed DNA sequences
gl2eigenstrat

Converts a genlight object into eigenstrat format
gl2treemix

Converts a genlight object to a treemix input file
gl2svdquartets

Converts a genlight object to nexus format PAUP SVDquartets
utils.recalc.avgpic

A utility function to recalculate intermediate locus metrics
utils.n.var.invariant

An internal utility function to calculate the number of variant and invariant sites by locus
utils.jackknife

An internal function to conducts jackknife resampling using a genlight object
utils.het.pop

An internal function that calculates expected mean heterozygosity per population
utils.transpose

An internal utility function to transpose a genlight object.
utils.vcfr2genlight.polyploid

Utility function to convert polyploid vcfR object as genlight
gl.check.wd

Checks the global working directory
gl.alf

Calculates allele frequency of the first and second allele for each locus A very simple function to report allele frequencies
gl.Ho

Estimates observed Heterozygosity
gl.He

Estimates expected Heterozygosity
gl.amova

Performs AMOVA using genlight data
gl.colors

Returns a list of colors for use in plots
cbind.dartR

adjust cbind for dartR
gl.check.verbosity

Checks the current global verbosity
gl.add.indmetrics

Adds metadata into a genlight object
gl.allele.freq

Generates percentage allele frequencies by locus and population