Man pages for dartR.base
Analysing 'SNP' and 'Silicodart' Data - Basic Functions
| cbind.dartR | adjust cbind for dartR |
| gl2bayesAss | Converts a genlight object into bayesAss (BA3) input format |
| gl2bayescan | Converts a genlight object into a format suitable for input... |
| gl2bpp | Converts a genlight object into a format suitable for input... |
| gl2demerelate | Creates a dataframe suitable for input to package... |
| gl2eigenstrat | Converts a genlight object into eigenstrat format |
| gl2fasta | Concatenates DArT trimmed sequences and outputs a FASTA file |
| gl2faststructure | Converts a genlight object into faststructure format (to run... |
| gl2gds | Converts a genlight object into gds format |
| gl2genalex | Converts a genlight object into a format suitable for input... |
| gl2genepop | Converts a genlight object into genepop format (and file) |
| gl2geno | Converts a genlight object to geno format from package LEA |
| gl2gi | Converts a genind object into a genlight object |
| gl2hiphop | Converts a genlight objects into hiphop format |
| gl2paup.parsimony | Converts a genlight object to nexus format for parsimony... |
| gl2paup.svdquartets | Converts a genlight object to nexus format PAUP SVDquartets |
| gl2phylip | Creates a Phylip input distance matrix from a genlight (SNP)... |
| gl2plink | Converts a genlight object into PLINK format |
| gl2related | Converts a genlight object to format suitable to be run with... |
| gl2sa | Converts genlight objects to the format used in the SNPassoc... |
| gl2snapper | Converts a genlight object to nexus format suitable for... |
| gl2structure | Converts a genlight object to STRUCTURE formatted files |
| gl2treemix | Converts a genlight object to a treemix input file |
| gl2vcf | Converts a genlight object into vcf format |
| gl.add.indmetrics | Adds metadata into a genlight object |
| gl.alf | Calculates allele frequency of the first and second allele... |
| gl.allele.freq | Generates percentage allele frequencies by locus and... |
| gl.amova | Performs AMOVA using genlight data |
| gl.check.verbosity | Checks the current global verbosity |
| gl.check.wd | Checks the global working directory |
| gl.colors | Returns a list of colors for use in plots |
| gl.compliance.check | Checks a genlight object to see if it complies with dartR... |
| gl.define.pop | Defines a new population in a genlight object for specified... |
| gl.diagnostics.hwe | Provides descriptive stats and plots to diagnose potential... |
| gl.dist.ind | Calculates a distance matrix for individuals defined in a... |
| gl.dist.phylo | Generates a distance matrix from a SNP genlight object taking... |
| gl.dist.pop | Calculates a distance matrix for populations with SNP or... |
| gl.drop.ind | Removes specified individuals from a dartR genlight object |
| gl.drop.loc | Removes specified loci from a dartR genlight object |
| gl.drop.pop | Removes specified populations from a dartR genlight object |
| gl.edit.recode.ind | Creates or edits individual (=specimen) names, creates a... |
| gl.edit.recode.pop | Creates or edits and applies a population re-assignment table |
| gl.fdsim | Estimates the rate of false positives in a fixed difference... |
| gl.filter.allna | Filters loci that are all NA across individuals and/or... |
| gl.filter.callrate | Filters loci or specimens in a genlight {adegenet} object... |
| gl.filter.excess.het | Filters excessively-heterozygous loci from a genlight object |
| gl.filter.factorloadings | Filters loci based on factor loadings for a PCA or PCoA |
| gl.filter.hamming | Filters loci based on pairwise Hamming distance between... |
| gl.filter.heterozygosity | Filters individuals with average heterozygosity greater than... |
| gl.filter.hwe | Filters loci that show significant departure from... |
| gl.filter.ld | Filters loci based on linkage disequilibrium (LD) |
| gl.filter.locmetric | Filters loci on the basis of numeric information stored in... |
| gl.filter.maf | Filters loci on the basis of minor allele frequency (MAF) or... |
| gl.filter.monomorphs | Filters monomorphic loci, including those with all NAs |
| gl.filter.overshoot | Filters loci for which the SNP has been trimmed from the... |
| gl.filter.pa | Filters loci that contain private (and fixed alleles) between... |
| gl.filter.rdepth | Filters loci based on counts of sequence tags scored at a... |
| gl.filter.reproducibility | Filters loci in a genlight {adegenet} object based on average... |
| gl.filter.secondaries | Filters loci that represent secondary SNPs in a genlight... |
| gl.filter.taglength | Filters loci in a genlight {adegenet} object based on... |
| gl.fixed.diff | Generates a matrix of fixed differences and associated... |
| gl.fst.pop | Calculates a pairwise Fst values for populations in a... |
| gl.He | Estimates expected Heterozygosity |
| gl.Ho | Estimates observed Heterozygosity |
| gl.hwe.pop | Performs Hardy-Weinberg tests over loci and populations |
| gl.impute | Imputes missing data |
| gl.join | Combines two dartR genlight objects |
| gl.keep.ind | Removes all but the specified individuals from a dartR... |
| gl.keep.loc | Removes all but the specified loci from a genlight object |
| gl.keep.pop | Removes all but the specified populations from a dartR... |
| gl.load | Loads an object from compressed binary format produced by... |
| gl.mahal.assign | Assigns individuals to populations with an associated... |
| gl.make.recode.ind | Creates a proforma recode_ind file for reassigning individual... |
| gl.make.recode.pop | Creates a proforma recode_pop_table file for reassigning... |
| gl.map.interactive | Creates an interactive map (based on latlon) from a genlight... |
| gl.merge.pop | Merges two or more populations in a dartR genlight object... |
| gl.pcoa | Ordination applied to genotypes in a genlight object (PCA),... |
| gl.pcoa.plot | Bivariate or trivariate plot of the results of an ordination... |
| gl.plot.heatmap | Represents a distance matrix as a heatmap |
| gl.print.history | Prints history of a genlight object |
| gl.prop.shared | Calculates a similarity (distance) matrix for individuals on... |
| gl.randomize.snps | Randomly changes the allocation of 0's and 2's in a genlight... |
| gl.read.csv | Reads SNP data from a csv file into a genlight object |
| gl.read.dart | Imports DArT data into dartR and converts it into a dartR... |
| gl.read.fasta | Reads FASTA files and converts them to genlight object |
| gl.read.PLINK | Reads PLINK data file into a genlight object |
| gl.read.silicodart | Imports presence/absence data from SilicoDArT to genlight... |
| gl.read.vcf | Converts a vcf file into a genlight object |
| gl.reassign.pop | Assigns an individual metric as pop in a genlight {adegenet}... |
| gl.recalc.metrics | Recalculates locus metrics when individuals or populations... |
| gl.recode.ind | Recodes individual (=specimen = sample) labels in a genlight... |
| gl.recode.pop | Recodes population assignments in a genlight object |
| gl.rename.pop | Renames a population in a genlight object |
| gl.report.allelerich | Report allelic richness per population from a genlight object |
| gl.report.allna | Reports loci that are all NA across individuals and/or... |
| gl.report.bases | Reports summary of base pair frequencies |
| gl.report.basics | Basic statistics for a genlight object |
| gl.report.callrate | Reports summary of Call Rate for loci or individuals |
| gl.report.diversity | Calculates diversity indexes for SNPs |
| gl.report.excess.het | Report loci with excess of heterozygosity |
| gl.report.factorloadings | Reports factor loadings for a PCA or PCoA |
| gl.report.fstat | Reports various statistics of genetic differentiation between... |
| gl.report.hamming | Calculates the pairwise Hamming distance between DArT trimmed... |
| gl.report.heterozygosity | Reports observed, expected and unbiased heterozygosities and... |
| gl.report.hwe | Reports departure from Hardy-Weinberg proportions |
| gl.report.ld | Calculates pairwise population based Linkage Disequilibrium... |
| gl.report.ld.map | Calculates pairwise linkage disequilibrium by population |
| gl.report.locmetric | Reports summary of the slot $other$loc.metrics |
| gl.report.maf | Reports minor allele frequency (MAF) for each locus in a SNP... |
| gl.report.monomorphs | Reports monomorphic loci |
| gl.report.overshoot | Reports loci for which the SNP has been trimmed from the... |
| gl.report.pa | Reports private alleles (and fixed alleles) per pair of... |
| gl.report.polyploid_heterozygosity | Reports observed, expected and unbiased heterozygosities and... |
| gl.report.rdepth | Reports summary of Read Depth for each locus |
| gl.report.replicates | Identify replicated individuals |
| gl.report.reproducibility | Reports summary of RepAvg (repeatability averaged over both... |
| gl.report.secondaries | Reports loci containing secondary SNPs in sequence tags and... |
| gl.report.shannon | Report SNP diversity from a genlight object, with reference... |
| gl.report.taglength | Reports summary of sequence tag length across loci |
| gl.sample | Samples individuals from populations |
| gl.save | Saves an object in compressed binary format for later rapid... |
| gl.select.colors | Selects colors from one of several palettes and outputs as a... |
| gl.select.shapes | Selects shapes from the base R shape palette and outputs as a... |
| gl.set.verbosity | Sets the default verbosity level |
| gl.set.wd | Sets the default working directory |
| gl.sim.cross | Generates random crosses between fathers and mothers |
| gl.sim.genotypes | Generate random genotypes |
| gl.smearplot | Smear plot |
| gl.sort | Sorts genlight objects |
| gl.subsample.ind | Subsample individuals from a genlight object |
| gl.subsample.loc | Subsample loci from a genlight object |
| gl.subsample.loci | Subsamples n loci from a genlight object and return it as a... |
| gl.test.heterozygosity | Tests the difference in heterozygosity between populations... |
| gl.tree.fitch | Generates a distance phylogeny |
| gl.tree.nj | Outputs a tree to summarize genetic similarity among... |
| gl.write.csv | Writes out data from a genlight object to csv file |
| rbind.dartR | adjust rbind for dartR |
| sub-dartR-ANY-ANY-ANY-method | indexing dartR objects correctly... |
| theme_dartR | Default theme for dartR plots |
| utils.basic.stats | Calculates mean observed heterozygosity, mean expected... |
| utils.check.datatype | Utility function to check the class of an object passed to a... |
| utils.collapse.matrix | Collapses a distance matrix calculated for individuals to a... |
| utils.dart2genlight | An internal function to converts DarT to genlight. |
| utils.dist.binary | Calculates a distance matrix for individuals defined in a... |
| utils.dist.ind.snp | Calculates a distance matrix for individuals defined in a... |
| utils.flag.start | A utility script to flag the start of a script |
| utils.hamming | Calculates the Hamming distance between two DArT trimmed DNA... |
| utils.het.pop | An internal function that calculates expected mean... |
| utils.impute | An internal script [Custodian to provide a title] |
| utils.is.fixed | An internal function to tests if two populations are fixed at... |
| utils.jackknife | An internal function to conducts jackknife resampling using a... |
| utils.n.var.invariant | An internal utility function to calculate the number of... |
| utils.plink.run | Runs PLINK from within R |
| utils.plot.save | An internal function to save a ggplot object to disk in RDS... |
| utils.read.dart | Utility to import DarT data to R |
| utils.read.fasta | An internal script to read a fastA file into a genlight... |
| utils.read.ped | An internal script [Custodian to provide a title] |
| utils.recalc.avgpic | A utility function to recalculate intermediate locus metrics |
| utils.recalc.callrate | A utility script to recalculate the callrate by locus after... |
| utils.recalc.freqhets | A utility script to recalculate the frequency of the... |
| utils.recalc.freqhomref | #' An internal utility function to recalculate the frequency... |
| utils.recalc.freqhomsnp | A utility function to recalculate the frequency of the... |
| utils.recalc.maf | A utility function to recalculate the minor allele frequency... |
| utils.reset.flags | #' An internal utility function to reset to FALSE (or TRUE)... |
| utils.transpose | An internal utility function to transpose a genlight object. |
| utils.vcfr2genlight.polyploid | Utility function to convert polyploid vcfR object as genlight |
| zzz | Setting up the package Setting theme, colors and verbosity |
