gi2gl |
Converts a genind object to genlight object |
gl.alf |
Calculates allele frequency of the first and second allele for each loci #' A very simple function to report allele frequencies |
gl.amova |
Performs and AMOVA using genlight data. |
gl.assign |
Assign an individual of unknown provenance to population |
gl.basic.stats |
Calculates basic statistics for each loci (Hs, Ho, Fis etc.) |
gl.collapse |
Collapse a distance matrix by amalgamating populations with pairwise fixed difference count less that a threshold |
gl.collapse.pval |
Collapse a fixed distance matrix by amalgamating populations for which pairwise fixed differences are not significant |
gl.collapse.recursive |
Recursively collapse a distance matrix by amalgamating populations |
gl.compliance.check |
Checks a gl object to see if it complies with dartR expectations, and amends to comply if necessary |
gl.costdistances |
Calculates cost distances for a given landscape (resistance matrix) |
gl.define.pop |
Define a new population in a genlight {adegenet} object on the basis of specified individuals |
gl.dist.ind |
Calculate a distance matrix for individuals defined in an {adegenet} genlight object |
gl.dist.pop |
Calculate a distance matrix for populations defined in an {adegenet} genlight object |
gl.drop.ind |
Remove specified individuals from a genelight {adegenet} object |
gl.drop.loc |
Remove specified loci from a genelight {adegenet} object |
gl.drop.pop |
Remove specified populations from a genelight {adegenet} object |
gl.edit.recode.ind |
Create or edit a individual (=specimen) names, create an recode_ind file amd apply the changes to a genlight object. |
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 |
gl.filter.cloneid |
Filter for CloneID to select only unique SNPs |
gl.filter.hamming |
Filters loci based on pairwise Hamming distance between sequence tags |
gl.filter.heterozygosity |
Filters individuals with average heterozygosity greater than a specified upper threshold or less than a specified lower threshold. |
gl.filter.hwe |
Filters loci that show significant departure from Hardy-Weinberg Equilibrium |
gl.filter.locmetric |
Filter loci on the basis of numeric information stored in other$loc.metrics in a genlight {adegenet} object |
gl.filter.maf |
Filter loci on the basis of minor allele frequency (MAF) in a genlight adegenet object |
gl.filter.monomorphs |
Remove 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 |
Filter loci that contain private (and fixed alleles) between two populations. |
gl.filter.parent.offspring |
Filter putative parent offspring within a population |
gl.filter.rdepth |
Filter loci based on counts of sequence tags scored at a locus (read depth) |
gl.filter.RepAvg |
Filter loci in a genlight {adegenet} object based on average repeatability of alleles at a locus |
gl.filter.reproducibility |
Filter loci in a genlight {adegenet} object based on average repeatability of alleles at a locus |
gl.filter.secondaries |
Filter loci that represent secondary SNPs in a genlight {adegenet} object |
gl.filter.sexlinked |
Identify loci that are sex linked in specimens in a genlight 'adegenet' object |
gl.filter.taglength |
Filter loci in a genlight {adegenet} object based on sequence tag length |
gl.fixed.diff |
Generate a matrix of fixed differences |
gl.fst.pop |
Calculate a pairwise fst values for populations in a genlight object |
gl.gene.freq |
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. |
gl.genleastcost |
Least-cost path analysis based on a friction matrix |
gl.grm |
Calculates an identity by descent matrix |
gl.grm.network |
Represents a genomic relatedness matrix as a network |
gl.He |
A very simple function to report expected Heterozygosity |
gl.Ho |
A very simple function to report observed Heterozygosity |
gl.hwe.pop |
Function to run Hardy-Weinberg tests over each loci and population |
gl.ibd |
Isolation by distance |
gl.install.vanilla.dartR |
This functions installs all required packages for using all functions available in dartR The function compares the installed packages with the the currently available ones on cran. Be aware this function only works if a version of dartR is already installed on your system. You can choose if you also want to have a specific version of dartR installed ("CRAN", "master" or "dev" ). "master" and "dev" are installed from Github. Be aware the dev version from github is not fully tested and most certainly will contain untested functions. |
gl.join |
Combines two genlight objects |
gl.keep.ind |
Remove all but the specified individuals from a genelight {adegenet} object |
gl.keep.loc |
Remove all but the specified loci from a genelight {adegenet} object |
gl.keep.pop |
Remove all but specified populations from a genelight {adegenet} object |
gl.load |
Retrieves an object in compressed binary format earlier saved using gl.save. |
gl.make.recode.ind |
Create a proforma recode_ind file for reassigning individual (=specimen) names |
gl.make.recode.pop |
Create a proforma recode_pop_table file for reassigning population names |
gl.map.interactive |
Creates an interactive map (based on latlong) from a genlight object |
gl.merge.pop |
Merge two or more populations in a genelight {adegenet} object into one population |
gl.nhybrids |
Create an input file for the program NewHybrids and run it if NewHybrids is installed |
gl.outflank |
Function to identify loci under selection per population using the outflank method of Whitlock and Lotterhos (2015) |
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 plot of the results of an ordination generated using gl.pcoa() |
gl.pcoa.plot.3d |
3D interactive plot of the results of a PCoA ordination |
gl.pcoa.scree |
Produce a plot of eigenvalues, standardized as percentages, derived from a PCoA |
gl.percent.freq |
Generate percentage allele frequencies by locus and population |
gl.play.history |
Replays the history and applies it to a genlight object |
gl.plot |
Plotting genlight object as a smear plot (loci by individuals color coded for scores of 0, 1, 2 and NA) |
gl.plot.heatmap |
Represent a distance matrix as a heatmap |
gl.plot.network |
Represents a distance or dissimilarity matrix as a network |
gl.print.history |
Prints history of a genlight object |
gl.propShared |
Calculate a similarity(distance) matrix for individuals on the proportion of shared alleles |
gl.read.csv |
Read SNP data from a csv file into a genlight object |
gl.read.dart |
Import DarT data into R and conver it to a genlight object |
gl.read.silicodart |
Import presence/absence data from SilicoDArT to genlight {agegenet} format (ploidy=1) |
gl.read.vcf |
Converts a vcf file into a genlight object |
gl.reassign.pop |
Assign a individual metric as pop in a genlight {adegenet} object |
gl.recalc.metrics |
Recalculate locus metrics when individuals or populations are deleted from a genlight {adegenet} object |
gl.recode.ind |
Recode individual (=specimen = sample) labels in a genelight object {adegenet} |
gl.recode.pop |
Recode population assignments in a genlight object {adegenet} |
gl.report.bases |
Summary of base pair frequencies |
gl.report.callrate |
Report summary of Call Rate for loci or individuals |
gl.report.diversity |
Calculate diversity indices for SNPs |
gl.report.hamming |
Calculates the pairwise Hamming distance between DArT trimmed DNA sequences |
gl.report.heterozygosity |
Reports observed and expected heterozygosity by population or by individual from SNP data. |
gl.report.hwe |
Reports departure from Hardy-Weinberg Equilibrium |
gl.report.ld |
Calculates pairwise population based Linkage Disequilibirum across all loci using the specifyied number of cores |
gl.report.locmetric |
Report summary of the slot $other$loc.metrics |
gl.report.maf |
Report minor allele frequency (MAF) for each locus in a SNP dataset |
gl.report.monomorphs |
Report 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 |
Report private alleles (and fixed alleles) per pair of populations |
gl.report.parent.offspring |
Identify putative parent offspring within a population |
gl.report.rdepth |
Report summary of Read Depth for each locus |
gl.report.RepAvg |
Report summary of RepAvg averaged over both alleles for each locus or reproducibility (repeatability of the scores for fragment presence/absence). |
gl.report.reproducibility |
Report summary of RepAvg (repeatability averaged over both alleles for each locus) or reproducibility (repeatability of the scores for fragment presence/absence). |
gl.report.secondaries |
Report loci containing secondary SNPs in sequence tags |
gl.report.sexlinked |
Identify loci that are sex linked in specimens in a genlight 'adegenet' object |
gl.report.taglength |
Report summary of sequence tag length across loci in a genlight adegenet object |
gl.save |
Save an object in compressed binary format for later rapid retrieval. |
gl.set.verbosity |
Set the default verbosity level |
gl.sim.ind |
Simulates individuals based on the allele frequencies provided via a genlight object. |
gl.sim.offspring |
Simulates a specified number of offsprings based on alleles provided by potential father(s) and mother(s) |
gl.stockR |
Generate a SNP matrix from a genlight {adegenet} object for subsequent use in R package stockR. |
gl.subsample.loci |
Subsample n loci from a genlight object and return as a genlight object |
gl.test.heterozygosity |
Tests the difference in heterozyosity between populations taken pairwise. |
gl.tree.nj |
Output an nj tree to summarize genetic similarity among populations |
gl.utils.fdsim |
Estimate the rate of false positives in a fixed difference analysis |
gl.write.csv |
Write out data from a gl object adegenet to csv file |
gl2bayescan |
Convert a genlight object to format suitable for input to Bayescan |
gl2demerelate |
Create a dataframe suitable for input to package {Demerelate} from a genlight {adegenet} object |
gl2fasta |
Concatenates DArT trimmed sequences and outputs a fastA file. |
gl2faststructure |
Export DArT genlight object {adegenet} to faststructure format (to run faststructure elsewhere) |
gl2gds |
Convert a genlight object to gds format |
gl2genalex |
Convert a genlight object to format suitable for input to genalex |
gl2gi |
Converts a genlight object to genind object |
gl2hiphop |
Converts genlight objects to hiphop format |
gl2phylip |
Create a Phylip input distance matrix from a genlight (SNP) {adegenet} object |
gl2plink |
Converts a genlight object to PLINK file format |
gl2related |
Convert a genlight object to format suitable to be run with Coancestry |
gl2sa |
Convert genlight objects to the format used in the SNPassoc package |
gl2shp |
Convert genlight objects to ESRI shapefiles or kml files |
gl2snapp |
Convert a genlight object to nexus format suitable for phylogenetic analysis by SNAPP (via BEAUti) |
gl2structure |
Converts genlight objects to STRUCTURE formated files |
gl2svdquartets |
Convert a genlight object to nexus format PAUP SVDquartets |
gl2treemix |
Convert a genlight object to a treemix input file |
util.outflank |
OutFLANK: An Fst outlier approach by Mike Whitlock and Katie Lotterhos, University of British Columbia. |
util.outflank.MakeDiploidFSTMat |
Creates OutFLANK input file from individual genotype info. |
util.outflank.plotter |
Plotting functions for Fst distributions after OutFLANK This function takes the output of OutFLANK as input with the OFoutput parameter. It plots a histogram of the FST (by default, the uncorrected FSTs used by OutFLANK) of loci and overlays the inferred null histogram. |
utils.dart2genlight |
Convert DarT to genlight |
utils.dist.binary |
Calculate a distance matrix for individuals defined in an {adegenet} genlight object using binary P/A data (SilicoDArT) |
utils.hamming |
Calculates the Hamming distance between two DArT trimmed DNA sequences |
utils.hwe |
Calculates departure from Hardy-Weinberg Equilibrium. Utility script not meant for end users. |
utils.outflank |
OutFLANK: An Fst outlier approach by Mike Whitlock and Katie Lotterhos, University of British Columbia. |
utils.outflank.MakeDiploidFSTMat |
Creates OutFLANK input file from individual genotype info. |
utils.outflank.plotter |
Plotting functions for Fst distributions after OutFLANK This function takes the output of OutFLANK as input with the OFoutput parameter. It plots a histogram of the FST (by default, the uncorrected FSTs used by OutFLANK) of loci and overlays the inferred null histogram. |
utils.pa.ind |
Report number of private alleles possessed by an individual of unknown provenance |
utils.prob.hwe |
Exact SNP test of Hardy-Weinberg Equilibrium |
utils.read.dart |
Import DarT data to R |
utils.recalc.avgpic |
A utility script to recalculate the OneRatioRef, OneRatioSnp, PICRef, PICSnp, and AvgPIC by locus after some populations have been deleted. |
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 the frequency of the heterozygous SNPs by locus after some populations have been deleted |
utils.recalc.freqhomref |
A utility script to recalculate the the frequency of the homozygous reference SNP by locus after some populations have been deleted |
utils.recalc.freqhomsnp |
A utility script to recalculate the the frequency of the homozygous alternate SNP by locus after some populations have been deleted |
utils.recalc.maf |
A utility script to recalculate the the minor allele frequency by locus, typically after some populations have been deleted |
utils.reset.flags |
A utility script to reset to FALSE (or TRUE) the locus metric flags after some individuals or populations have been deleted. |