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

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

## Documentation for package ‘dartR.base’ version 1.2.3

- DESCRIPTION file

## Help Pages

C G I M R T U Z misc

## -- C --

cbind.dartR | cbind for dartR objects

## -- G --

gi2gl | Converts a genind object into a genlight object
gl.add.indmetrics | Adds metadata into a genlight object
gl.alf | Calculates allele frequency of the first and second allele for each locus A very simple function to report allele frequencies
gl.allele.freq | Generates percentage allele frequencies by locus and population
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 expectations and amends it to comply if necessary @family environment
gl.define.pop | Defines a new population in a genlight object for specified individuals
gl.diagnostics.hwe | Provides descriptive stats and plots to diagnose potential problems with Hardy-Weinberg proportions
gl.dist.ind | Calculates a distance matrix for individuals defined in a genlight object
gl.dist.phylo | Generates a distance matrix from a SNP genlight object taking into account a substitution model
gl.dist.pop | Calculates a distance matrix for populations with SNP or Silicodart genotypes in a genlight object
gl.document | Generate a roxygen2 Documentation Template for a Function
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 recode_ind file and applies the changes to a genlight object @family data manipulation
gl.edit.recode.pop | Creates or edits and applies a population re-assignment table
gl.fbm2gen | Convert an FBM-backed dartR to a GEN-backed dartR (streamed with big_apply)
gl.fdsim | Estimates the rate of false positives in a fixed difference analysis
gl.filter.allna | Filters loci that are all NA across individuals and/or populations with all NA across loci
gl.filter.callrate | Filters loci or specimens in a genlight {adegenet} object based on call rate
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 by trimmed-sequence similarity using Hamming distance
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.filter.hwe | Filters loci that show significant departure from Hardy-Weinberg Equilibrium @family matched filter
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.filter.maf | Filters loci on the basis of minor allele frequency (MAF) or minor allele count (MAC)
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 sequence tag along with the adaptor
gl.filter.pa | Filters loci that contain private (and fixed alleles) between two populations
gl.filter.rdepth | Filters loci based on counts of sequence tags scored at a locus (read depth) @family matched filter
gl.filter.replicates | Remove replicated individuals
gl.filter.reproducibility | Filters loci in a genlight {adegenet} object based on average repeatability of alleles at a locus @family matched filter
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.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.gen2fbm | Convert a gen-backed object to FBM-backed (streamed with big_apply)
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 genlight object
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 genlight object
gl.load | Loads an object from compressed binary format produced by gl.save()
gl.mahal.assign | Assigns individuals to populations with an associated probability
gl.make.recode.ind | Creates a proforma recode_ind file for reassigning individual (=specimen) names
gl.make.recode.pop | Creates a proforma recode_pop_table file for reassigning population names @family data manipulation
gl.map.interactive | Creates an interactive map (based on latlon) from a genlight object
gl.merge.pop | Merges two or more populations in a dartR genlight object into one population
gl.pcoa | Ordination applied to genotypes in a genlight object (PCA), in an fd object, or to a distance matrix (PCoA)
gl.pcoa.plot | Bivariate or trivariate plot of the results of an ordination generated using gl.pcoa()
gl.plot.heatmap | Represents a distance matrix as a heatmap
gl.plot.snp.density | Plot SNP density along chromosomes (heat-map)
gl.print.history | Prints history of a genlight object
gl.prop.shared | Calculates a similarity (distance) matrix for individuals on the proportion of shared alleles @family distance
gl.propShared | Calculates a similarity (distance) matrix for individuals on the proportion of shared alleles @family distance
gl.randomize.snps | Randomly changes the allocation of 0's and 2's in a genlight object
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 genlight object
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 {agegenet} format (ploidy=1)
gl.read.vcf | Converts a vcf file into a genlight object
gl.reassign.ind | Reassign specified individuals to a (new or existing) population
gl.reassign.pop | Assigns an individual attribute in ind.metrics as pop in a genlight {adegenet} object
gl.recalc.metrics | Recalculates locus metrics when individuals or populations are deleted from a genlight {adegenet} object @family environment
gl.recode.ind | Recodes individual (=specimen = sample) labels in a genlight object
gl.recode.pop | Recodes population assignments in a genlight object
gl.rename.pop | Renames a population in a genlight object
gl.report.allelerich | Reports allelic richness per population from a genlight object
gl.report.allna | Reports loci that are all NA across individuals and/or populations with all NA across loci
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 populations with confidence intervals
gl.report.hamming | Calculates the pairwise Hamming distance between DArT trimmed DNA sequences
gl.report.heterozygosity | Reports observed, expected and unbiased heterozygosities and FIS (inbreeding coefficient) by population or by individual from SNP data
gl.report.hwe | Reports departure from Hardy-Weinberg proportions
gl.report.ld | Calculates pairwise population based Linkage Disequilibrium across all loci using the specified number of cores @family matched report
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 dataset
gl.report.monomorphs | Reports monomorphic loci
gl.report.overshoot | Reports loci for which the SNP has been trimmed from the sequence tag along with the adaptor
gl.report.pa | Reports private alleles (and fixed alleles) per pair of populations
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.report.replicates | Identify replicated individuals
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.report.secondaries | Reports loci containing secondary SNPs in sequence tags and calculates number of invariant sites
gl.report.shannon | Report SNP diversity from a genlight object, with reference to Ma, Z., Li, L., & Zhang, Y. P. (2020). Defining individual-level genetic diversity and similarity profiles. Scientific reports, 10(1), 5805.
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 retrieval
gl.select.colors | Selects colors from one of several palettes and outputs as a vector
gl.select.shapes | Selects shapes from the base R shape palette and outputs as a vector
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.crosses | Generates random crosses between fathers and mothers
gl.sim.genotypes | Generate random genotypes
gl.smearplot | Smear plot
gl.sort | Sorts genlight objects by individual, population, or genomic position
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 genlight object
gl.test.heterozygosity | Tests the difference in heterozygosity between populations taken pairwise
gl.tree.fitch | Generates a distance phylogeny
gl.tree.nj | Outputs a tree to summarize genetic similarity among populations (e.g. phenogram)
gl.write.csv | Writes out data from a genlight object to csv file
gl2bayesAss | Converts a genlight object into bayesAss (BA3) input format
gl2bayescan | Converts a genlight object into a format suitable for input to Bayescan
gl2bpp | Converts a genlight object into a format suitable for input to the BPP program
gl2demerelate | Creates a dataframe suitable for input to package {Demerelate} from a genlight {adegenet} object
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 faststructure elsewhere)
gl2gapit | Converts a genlight object to geno format from package LEA
gl2gds | Converts a genlight object into gds format
gl2genalex | Converts a genlight object into a format suitable for input to genalex
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
gl2hapmap | Converts a genlight object into HapMap format
gl2hiphop | Converts a genlight objects into hiphop format
gl2paup.parsimony | Converts a genlight object to nexus format for parsimony phylogeny analysis in PAUP and, optionally produces accompanying files for parallel processing.
gl2paup.svdquartets | Converts a genlight object to nexus format PAUP SVDquartets
gl2phylip | Creates a Phylip input distance matrix from a genlight (SNP) {adegenet} object
gl2plink | Converts a genlight object into PLINK format
gl2related | Converts a genlight object to format suitable to be run with Coancestry
gl2snapper | Converts a genlight object to nexus format suitable for phylogenetic analysis by Snapper (via BEAUti)
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
glMean | glMean for dartR objects
glSum | glSum for dartR objects

## -- I --

ind.count | An internal function that calculates expected mean heterozygosity per population

## -- M --

matrix2gen | An internal script [Custodian to provide a title]

## -- R --

rbind.dartR | rbind for dartR objects

## -- T --

theme_dartR | Default theme for dartR plots

## -- U --

utils.allelic.richness | A utility script to calculate allelic richness using bootstraping
utils.basic.stats | Calculates mean observed heterozygosity, mean expected heterozygosity and FIS per locus, per population and various population differentiation measures @family utilities
utils.check.datatype | Utility function to check the class of an object passed to a function
utils.collapse.matrix | Collapses a distance matrix calculated for individuals to a distance matrix for populations defined in a dartR genlight object
utils.dart2genlight | An internal function to converts DarT to genlight.
utils.dist.binary | Calculates a distance matrix for individuals defined in a dartR genlight object using binary P/A data (SilicoDArT)
utils.dist.ind.snp | Calculates a distance matrix for individuals defined in a genlight object using SNP data (DArTseq)
utils.flag.start | A utility script to flag the start of a script
utils.hamming | Calculates the Hamming distance between two DArT trimmed DNA sequences
utils.heatmap | Enhanced Heat Map
utils.het.pop | An internal function that calculates expected mean heterozygosity per population
utils.impute | An internal script [Custodian to provide a title]
utils.is.fixed | An internal function to tests if two populations are fixed at a given locus
utils.jackknife | An internal function to conducts jackknife resampling using a genlight object
utils.n.var.invariant | An internal utility function to calculate the number of variant and invariant sites by locus
utils.plink.run | Runs PLINK from within R
utils.plot.save | An internal function to save a ggplot object to disk in RDS binary format
utils.read.dart | Utility to import DarT data to R
utils.read.fasta | An internal script to read a fastA file into a genlight object
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 some populations have been deleted
utils.recalc.freqhets | A utility script to recalculate the frequency of the heterozygous SNPs by locus after some populations have been deleted
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.recalc.freqhomsnp | A utility function to recalculate the frequency of the homozygous alternate SNP by locus after some 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.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.transpose | An internal utility function to transpose a genlight object.
utils.vcfr2genlight.polyploid | Utility function to convert polyploid vcfR object as genlight

## -- Z --

zzz | Setting up the package Setting theme, colors and verbosity

## -- misc --

[-method | indexing dartR objects correctly...