Man pages for adegenet
Exploratory Analysis of Genetic and Genomic Data

accessorsAccessors for adegenet objects
adegenet.packageThe adegenet package
AICcCompute Akaike Information Criterion for small samples (AICc)...
AIC.snapclustCompute Akaike Information Criterion (AIC) for snapclust
ascoreCompute and optimize a-score for Discriminant Analysis of...
as.genlightConversion to class "genlight"
as-methodsConverting genind/genpop objects to other classes
as.SNPbinConversion to class "SNPbin"
auxilAuxiliary functions for adegenet
BIC.snapclustCompute Bayesian Information Criterion (BIC) for snapclust
chooseCNFunction to choose a connection network
colorplotRepresents a cloud of points with colors
compoplotGenotype composition plot
coords.monmonierReturns original points in results paths of an object of...
dapcDiscriminant Analysis of Principal Components (DAPC)
dapcGraphicsGraphics for Discriminant Analysis of Principal Components...
dapcIllusSimulated data illustrating the DAPC
df2genindConvert a data.frame of allele data to a genind object.
dist.genpopGenetic distances between populations
doc_C_routinesInternal C routines
eHGDPExtended HGDP-CEPH dataset
export_to_mvmapperExport analysis for mvmapper visualisation
fasta2DNAbinRead large DNA alignments into R
fasta2genlightExtract Single Nucleotide Polymorphism (SNPs) from alignments
find.clustersfind.cluster: cluster identification using successive K-means
gengraphGenetic transitive graphs
genindadegenet formal class (S4) for individual genotypes
genind2dfConvert a genind object to a data.frame.
genind2genpopConversion from a genind to a genpop object
genlightFormal class "genlight"
genpopadegenet formal class (S4) for allele counts in populations
glAuxAuxiliary functions for genlight objects
glPcaPrincipal Component Analysis for genlight objects
glPlotPlotting genlight objects
glSimSimulation of simple genlight objects
H3N2Seasonal influenza (H3N2) HA segment data
haploGenSimulation of genealogies of haplotypes
hierarchy-methodsAccess and manipulate the population hierarchy for genind or...
HsExpected heterozygosity (Hs)
Hs.testTest differences in expected heterozygosity (Hs)
HWEHardy-Weinberg Equilibrium test for multilocus data
hybridizeFunction hybridize takes two genind in inputs and generates...
hybridtoyToy hybrid dataset
import2genindImporting data from several softwares to a genind object
inbreedingLikelihood-based estimation of inbreeding
isPolyAssess polymorphism in genind/genpop objects
KICCompute Akaike Information Criterion for small samples (AICc)...
loadingplotRepresents a cloud of points with colors
makefreqCompute allelic frequencies
microbovMicrosatellites genotypes of 15 cattle breeds
minorAlleleCompute minor allele frequency
monmonierBoundary detection using Monmonier algorithm
mutationsIdentify mutations between DNA sequences
nancycatsMicrosatellites genotypes of 237 cats from 17 colonies of...
new.genindgenind constructor
new.genpopgenpop constructor
old2newConvert objects with obsolete classes into new objects
pairDistPairwise distance plots
population-methodsManipulate the population factor of genind objects.
propSharedCompute proportion of shared alleles
propTypedCompute the proportion of typed elements
read.fstatReading data from Fstat
read.genepopReading data from Genepop
read.genetixReading data from GENETIX
read.PLINKReading PLINK Single Nucleotide Polymorphism data
read.snpReading Single Nucleotide Polymorphism data
read.structureReading data from STRUCTURE
repoolPool several genotypes into a single dataset
rupicaMicrosatellites genotypes of 335 chamois (Rupicapra...
scaleGenCompute scaled allele frequencies
selpopsizeSelect genotypes of well-represented populations
seplocSeparate data per locus
seppopSeparate genotypes per population
seqTrackSeqTrack algorithm for reconstructing genealogies
sequencesImporting data from an alignement of sequences to a genind...
serversWeb servers for adegenet
showmekittensWhen you need a break...
sim2popSimulated genotypes of two georeferenced populations
snapclustMaximum-likelihood genetic clustering using EM algorithm
snapclust.choose.kChoose the number of clusters for snapclust using AIC, BIC or...
SNPbinFormal class "SNPbin"
snpposiAnalyse the position of polymorphic sites
snpzipIdentification of structural SNPs
spcaSpatial principal component analysis
spcaIllusSimulated data illustrating the sPCA
spca_randtestMonte Carlo test for sPCA
spca.rtestsGlobal and local tests
strata-methodsAccess and manipulate the population strata for genind or...
swallowtailsMicrosatellites genotypes of 781 swallowtail butterflies from...
tabAccess allele counts or frequencies
truenamesRestore true labels of an object
virClassesVirtual classes for adegenet
webFunctions to access online resources for adegenet
xvalDapcCross-validation for Discriminant Analysis of Principal...
adegenet documentation built on Feb. 16, 2023, 6 p.m.