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 |
gl.collapse.pval |
Collapse a fixed distance matrix by amalgamating populations for which fixed differences are not significant |
gl.collapse.recursive |
Recursively collapse a distance matrix by amalgamating populations |
gl.costdistances |
Calculates cost distances for a given landscape (resistance matrix) |
gl.define.pop |
Define a new population in a genelight {adegenet} object on the basis of specified individuals |
gl.dist.heatmap |
Represent a distance matrix as a heatmap |
gl.dist.pop |
Calculate a distance matrix for populations defined in an {adegenet} genlight object |
gl.diversity |
Calculate diversity indices for SNPs |
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 and create an recode_ind file |
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 in a genlight object based on pairwise Hamming distance between sequence tags |
gl.filter.hwe |
Filters loci that show significant departure from Hardy-Weinberg Equilibrium |
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.repavg |
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.fixed.diff |
Generate a matrix of fixed differences from a genelight or genind object {adegenet} |
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 the genomic relatedness matrix |
gl.grm.network |
Represents a genomic relatedness matrix as a network |
gl.Ho |
A very simple function to report observed Heterozygosity |
gl.Hs |
A very simple function to report expected Heterozygosity |
gl.hwe.pop |
Filter function to facilitate analysing of dart data |
gl.ibd |
Isolation by distance |
gl.keep.ind |
Remove all but the specified individuals from a genelight {adegenet} object |
gl.keep.pop |
Remove all but specified populations from a genelight {adegenet} object |
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 |
PCoA ordination (glPca) |
gl.pcoa.plot |
Bivariate plot of the results of a PCoA ordination |
gl.pcoa.plot.3d |
3D interactive plot of the results of a PCoA ordination |
gl.pcoa.pop |
PCoA ordination of populations |
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.plot |
Plotting genlight object |
gl.read.dart |
Import DarT data into R and conver it to a genlight object |
gl.read.dart.2row |
Import SNP data from DArT and convert to genlight {agegenet} format (gl) |
gl.read.silicodart |
Import presence/absence data from SilicoDArT and convert to genind {agegenet} format |
gl.recalc.metrics |
Recalculate locus metrics when individuals or populations are deleted from a genlight {adegenet} object |
gl.recode.ind |
Recode individual (=specimen) labels in a genelight or genind object {adegenet} |
gl.recode.pop |
Recode population assignments in a genelight object {adegenet} |
gl.report.bases |
Summary of base pair frequencies |
gl.report.callrate |
Report summary of Call Rate for loci or individuals |
gl.report.hamming |
Calculates the pairwise Hamming distance between DArT trimmed DNA sequences |
gl.report.heterozygosity |
Reports hetrozygosity |
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.maf |
Report minor allele frequency (MAF) for each locus in a genlight adegenet object |
gl.report.monomorphs |
Report monomorphic loci, including those with all NAs |
gl.report.pa |
Report number of private alleles possessed by an individual of unknown provenance |
gl.report.pa.pop |
Report private alleles (and fixed alleles) per pair of populations |
gl.report.repavg |
Report summary of RepAvg, reproducibility averaged over both alleles for each locus in a genlight adegenet object |
gl.report.secondaries |
Report loci containing secondary SNPs in a genlight {adegenet} object |
gl.sexlinkage |
Identify loci that are sex linked in specimens in a genlight {adegenet} object |
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.subsample.loci |
Subsample n loci from a genlight object and return as a genlight object |
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 |
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 nexus format PAUP SVDquartets |
gl2gi |
Converts a genlight object to genind object |
gl2phylip |
Create a Phylip input distance matrix from a genlight (SNP) or genind (SilicoDarT) {adegenet} object |
gl2plink |
Converts a genlight object to plink file format |
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 |