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dartR.base  

Analysing 'SNP' and 'Silicodart' Data - Basic Functions
View on CRAN: Click here


Download and install dartR.base package within the R console
Install from CRAN:
install.packages("dartR.base")

Install from Github:
library("remotes")
install_github("cran/dartR.base")

Install by package version:
library("remotes")
install_version("dartR.base", "0.65")



Attach the package and use:
library("dartR.base")
Maintained by
Bernd Gruber
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2023-08-12
Latest Update: 2023-11-17
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.
How to cite:
Bernd Gruber (2023). dartR.base: Analysing 'SNP' and 'Silicodart' Data - Basic Functions. R package version 0.65, https://cran.r-project.org/web/packages/dartR.base
Previous versions and publish date:
0.49 (2023-08-12 17:00)
Other packages that cited dartR.base R package
View dartR.base citation profile
Other R packages that dartR.base depends, imports, suggests or enhances
Functions, R codes and Examples using the dartR.base R package
Some associated functions: bandicoot.gl . cbind.dartR . gl.He . gl.Ho . gl.alf . gl.allele.freq . gl.amova . gl.check.verbosity . gl.check.wd . gl.colors . gl.compliance.check . gl.define.pop . gl.diagnostics.hwe . gl.dist.ind . gl.dist.pop . gl.drop.ind . gl.drop.loc . gl.drop.pop . gl.edit.recode.ind . gl.edit.recode.pop . gl.fdsim . gl.filter.allna . gl.filter.callrate . gl.filter.factorloadings . gl.filter.hamming . gl.filter.heterozygosity . gl.filter.hwe . gl.filter.ld . gl.filter.locmetric . gl.filter.maf . gl.filter.monomorphs . gl.filter.overshoot . gl.filter.pa . gl.filter.rdepth . gl.filter.reproducibility . gl.filter.secondaries . gl.filter.taglength . gl.fixed.diff . gl.fst.pop . gl.hwe.pop . gl.impute . gl.join . gl.keep.ind . gl.keep.loc . gl.keep.pop . gl.load . gl.mahal.assign . gl.make.recode.ind . gl.make.recode.pop . gl.map.interactive . gl.merge.pop . gl.pcoa . gl.pcoa.plot . gl.plot.heatmap . gl.print.history . gl.prop.shared . gl.randomize.snps . gl.read.PLINK . gl.read.csv . gl.read.dart . gl.read.fasta . gl.read.silicodart . gl.read.vcf . gl.reassign.pop . gl.recalc.metrics . gl.recode.ind . gl.recode.pop . gl.rename.pop . gl.report.bases . gl.report.basics . gl.report.callrate . gl.report.diversity . gl.report.factorloadings . gl.report.fstat . gl.report.hamming . gl.report.heterozygosity . gl.report.hwe . gl.report.ld.map . gl.report.ld . gl.report.locmetric . gl.report.maf . gl.report.monomorphs . gl.report.overshoot . gl.report.pa . gl.report.rdepth . gl.report.reproducibility . gl.report.secondaries . gl.report.taglength . gl.sample . gl.save . gl.select.colors . gl.select.shapes . gl.set.verbosity . gl.set.wd . gl.sim.cross . gl.sim.genotypes . gl.smearplot . gl.sort . gl.subsample.ind . gl.subsample.loc . gl.test.heterozygosity . gl.tree.nj . gl.write.csv . gl2bayesAss . gl2bayescan . gl2bpp . gl2demerelate . gl2eigenstrat . gl2fasta . gl2faststructure . gl2gds . gl2genalex . gl2genepop . gl2geno . gl2gi . gl2hiphop . gl2phylip . gl2plink . gl2related . gl2sa . gl2snapp . gl2structure . gl2svdquartets . gl2treemix . gl2vcf . possums.gl . rbind.dartR . sub-dartR-ANY-ANY-ANY-method . testset.gl . testset.gs . theme_dartR . utils.basic.stats . utils.check.datatype . utils.dart2genlight . utils.dist.binary . utils.dist.ind.snp . utils.flag.start . utils.hamming . utils.het.pop . utils.impute . utils.is.fixed . utils.jackknife . utils.n.var.invariant . utils.plink.run . utils.plot.save . utils.read.dart . utils.read.fasta . utils.read.ped . utils.recalc.avgpic . utils.recalc.callrate . utils.recalc.freqhets . utils.recalc.freqhomref . utils.recalc.freqhomsnp . utils.recalc.maf . utils.reset.flags . utils.transpose . zzz . 
Some associated R codes: Full dartR.base package functions and examples
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