adegenet: Exploratory Analysis of Genetic and Genomic Data

Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.

Install the latest version of this package by entering the following in R:
AuthorThibaut Jombart, Zhian N. Kamvar, Roman Lustrik, Caitlin Collins, Marie- Pauline Beugin, Brian Knaus, Peter Solymos, Klaus Schliep, Ismail Ahmed, Anne Cori, Federico Calboli
Date of publication2016-02-15 16:12:41
MaintainerThibaut Jombart <>
LicenseGPL (>= 2)

View on CRAN

Man pages

accessors: Accessors for adegenet objects

adegenet.package: The adegenet package

ascore: Compute and optimize a-score for Discriminant Analysis of...

as.genlight: Conversion to class "genlight"

as-methods: Converting genind/genpop objects to other classes

as.SNPbin: Conversion to class "SNPbin"

auxil: Auxiliary functions for adegenet

chooseCN: Function to choose a connection network

colorplot: Represents a cloud of points with colors

coords.monmonier: Returns original points in results paths of an object of...

dapc: Discriminant Analysis of Principal Components (DAPC)

dapcGraphics: Graphics for Discriminant Analysis of Principal Components...

dapcIllus: Simulated data illustrating the DAPC

df2genind: Convert a data.frame of allele data to a genind object.

dist.genpop: Genetic distances between populations

eHGDP: Extended HGDP-CEPH dataset

fasta2DNAbin: Read large DNA alignments into R

fasta2genlight: Extract Single Nucleotide Polymorphism (SNPs) from alignments

find.clusters: find.cluster: cluster identification using successive K-means

gengraph: Genetic transitive graphs

genind: adegenet formal class (S4) for individual genotypes

genind2df: Convert a genind object to a data.frame.

genind2genpop: Conversion from a genind to a genpop object

genlight: Formal class "genlight"

genpop: adegenet formal class (S4) for allele counts in populations

glAux: Auxiliary functions for genlight objects

glPca: Principal Component Analysis for genlight objects

glPlot: Plotting genlight objects

glSim: Simulation of simple genlight objects

H3N2: Seasonal influenza (H3N2) HA segment data

haploGen: Simulation of genealogies of haplotypes

hierarchy-methods: Access and manipulate the population hierarchy for genind or...

Hs: Expected heterozygosity (Hs)

Hs.test: Test differences in expected heterozygosity (Hs)

HWE: Hardy-Weinberg Equilibrium test for multilocus data

hybridize: Function hybridize takes two genind in inputs and generates...

import2genind: Importing data from several softwares to a genind object

inbreeding: Likelihood-based estimation of inbreeding

isPoly: Assess polymorphism in genind/genpop objects

loadingplot: Represents a cloud of points with colors

makefreq: Compute allelic frequencies

microbov: Microsatellites genotypes of 15 cattle breeds

minorAllele: Compute minor allele frequency

monmonier: Boundary detection using Monmonier algorithm

mutations: Identify mutations between DNA sequences

nancycats: Microsatellites genotypes of 237 cats from 17 colonies of...

new.genind: genind constructor

new.genpop: genpop constructor

old2new: Convert objects with obsolete classes into new objects

pairDist: Pairwise distance plots

population-methods: Manipulate the population factor of genind objects.

propShared: Compute proportion of shared alleles

propTyped: Compute the proportion of typed elements

read.fstat: Reading data from Fstat

read.genepop: Reading data from Genepop

read.genetix: Reading data from GENETIX

read.PLINK: Reading PLINK Single Nucleotide Polymorphism data

read.snp: Reading Single Nucleotide Polymorphism data

read.structure: Reading data from STRUCTURE

repool: Pool several genotypes into a single dataset

rupica: Microsatellites genotypes of 335 chamois (Rupicapra...

scaleGen: Compute scaled allele frequencies

selpopsize: Select genotypes of well-represented populations

seploc: Separate data per locus

seppop: Separate genotypes per population

seqTrack: SeqTrack algorithm for reconstructing genealogies

sequences: Importing data from an alignement of sequences to a genind...

servers: Web servers for adegenet

sim2pop: Simulated genotypes of two georeferenced populations

SNPbin: Formal class "SNPbin"

snpposi: Analyse the position of polymorphic sites

spca: Spatial principal component analysis

spcaIllus: Simulated data illustrating the sPCA

spca.rtests: Global and local tests

strata-methods: Access and manipulate the population strata for genind or...

tab: Access allele counts or frequencies

truenames: Restore true labels of an object

virClasses: Virtual classes for adegenet

web: Functions to access online resources for adegenet

xvalDapc: Cross-validation for Discriminant Analysis of Principal...


addStrata Man page
addStrata<- Man page
addStrata<-,genind-method Man page
addStrata,genind-method Man page
addStrata<-,genlight-method Man page
addStrata,genlight-method Man page
adegenet Man page
adegenetIssues Man page
adegenet.package Man page
adegenet.package-package Man page
adegenetServer Man page
adegenetTutorial Man page
adegenetWeb Man page
alignment2genind Man page
alleles Man page
alleles<- Man page
alleles<-,genind-method Man page
alleles,genind-method Man page
alleles<-,genlight-method Man page
alleles,genlight-method Man page
alleles<-,gen-method Man page
alleles,gen-method Man page
alleles<-,genpop-method Man page
alleles,genpop-method Man page
any2col Man page
a.score Man page Man page Man page
as,data.frame,genlight-method Man page Man page
as.genind Man page
as,genind,data.frame-method Man page
as,genind,genpop-method Man page
as,genind,ktab-method Man page
as,genind,matrix-method Man page
as.genlight Man page
as,genlight,data.frame-method Man page
as.genlight,data.frame-method Man page
as,genlight,list-method Man page
as.genlight,list-method Man page
as,genlight,matrix-method Man page
as.genlight,matrix-method Man page
as,genlight,snp.matrix-method Man page
as.genlight,snp.matrix-method Man page
as.genpop Man page
as,genpop,data.frame-method Man page
as.genpop.genind Man page
as,genpop,ktab-method Man page
as,genpop,matrix-method Man page
as.igraph.haploGen Man page
as.igraph.seqTrack Man page
as.integer.SNPbin Man page
as,integer,SNPbin-method Man page
as.ktab.genind Man page
as.ktab.genpop Man page
as.lda Man page
as.lda.dapc Man page
as.list.genlight Man page
as,list,genlight-method Man page
as.matrix.genind Man page
as.matrix.genlight Man page
as,matrix,genlight-method Man page
as.matrix.genpop Man page
as-method Man page
as,numeric,SNPbin-method Man page
as.POSIXct.haploGen Man page
as,seqTrack,graphNEL-method Man page
as.seqTrack.haploGen Man page
assignplot Man page
as.SNPbin Man page
as,SNPbin,integer-method Man page
as.SNPbin,integer-method Man page
as,SNPbin,numeric-method Man page
as.SNPbin,numeric-method Man page
azur Man page
bluepal Man page
callOrNULL-class Man page
cbind.genlight Man page
cbind.SNPbin Man page
charOrNULL-class Man page
checkType Man page
chooseCN Man page
chr Man page
chr<- Man page
chr<-,genlight-method Man page
chr,genlight-method Man page
chromosome Man page
chromosome<- Man page
chromosome<-,genlight-method Man page
chromosome,genlight-method Man page
coerce,data.frame,genlight-method Man page
coerce,genind,data.frame-method Man page
coerce,genind,genpop-method Man page
coerce,genind,ktab-method Man page
coerce,genind,matrix-method Man page
coerce,genlight,data.frame-method Man page
coerce,genlight,list-method Man page
coerce,genlight,matrix-method Man page
coerce,genlight,snp.matrix-method Man page
coerce,genpop,data.frame-method Man page
coerce,genpop,ktab-method Man page
coerce,genpop,matrix-method Man page
coerce,integer,SNPbin-method Man page
coerce,list,genlight-method Man page
coerce,matrix,genlight-method Man page
coerce,numeric,SNPbin-method Man page
coerce,seqTrack,graphNEL-method Man page
coerce,SNPbin,integer-method Man page
colorplot Man page
colorplot.default Man page
colorplot.spca Man page
compoplot Man page
coords.monmonier Man page
corner Man page
c.SNPbin Man page
dapc Man page Man page
dapc.dudi Man page
dapc.genind Man page
dapc.genlight Man page
dapcIllus Man page
dapc.matrix Man page
deepseasun Man page
df2genind Man page
dfOrNULL-class Man page
dim,genlight-method Man page
dist.genpop Man page
dist,genpop,ANY,ANY,ANY,missing-method Man page
DNAbin2genind Man page
eHGDP Man page
extract.PLINKmap Man page
fac2col Man page
factorOrNULL-class Man page
fasta2DNAbin Man page
fasta2genlight Man page
find.clusters Man page Man page
find.clusters.genind Man page
find.clusters.genlight Man page
find.clusters.matrix Man page
findMutations Man page
findMutations.DNAbin Man page
.find.sub.clusters Man page
flame Man page
formOrNULL-class Man page
funky Man page
gen-class Man page
gengraph Man page
gengraph.default Man page
gengraph.dist Man page
gengraph.DNAbin Man page
gengraph.genind Man page
gengraph.genpop Man page
gengraph.matrix Man page
genind Man page
genind2df Man page
genind2genpop Man page
[,genind,ANY,ANY,ANY-method Man page
genind-class Man page
[,genind-method Man page
$<-,genind-method Man page
$,genind-method Man page
.genlab Man page
genlight Man page
[,genlight,ANY,ANY,ANY-method Man page
[,genlight,ANY,ANY-method Man page
genlight-class Man page
,genlight-method Man page
[,genlight-method Man page
$<-,genlight-method Man page
$,genlight-method Man page
genpop Man page
[,genpop,ANY,ANY,ANY-method Man page
genpop-class Man page
[,genpop-method Man page
$<-,genpop-method Man page
$,genpop-method Man page
get.likelihood Man page
get.likelihood.seqTrack Man page
glDotProd Man page
glMean Man page
glNA Man page
global.rtest Man page
glPca Man page
glPlot Man page
glSim Man page
glSum Man page
glVar Man page
graphMutations Man page
graphMutations.DNAbin Man page
greenpal Man page
greypal Man page
H3N2 Man page
haploGen Man page
[.haploGen Man page
haploGen-class Man page
hier Man page
hier<- Man page
hier<-,genind-method Man page
hier,genind-method Man page
hier<-,genlight-method Man page
hier,genlight-method Man page
Hs Man page
Hs.test Man page
HWE.test.genind Man page
hybridize Man page
import2genind Man page
inbreeding Man page
indInfo-class Man page
indNames Man page
indNames<- Man page
indNames<-,genind-method Man page
indNames,genind-method Man page
indNames<-,genlight-method Man page
indNames,genlight-method Man page
initialize,genind-method Man page
initialize,genind-methods Man page
initialize,genlight-method Man page
initialize,genpop-method Man page
initialize,genpop-methods Man page
initialize,SNPbin-method Man page
intOrNULL-class Man page
intOrNum-class Man page
is.genind Man page
is.genpop Man page
isPoly Man page
isPoly,genind-method Man page
isPoly,genpop-method Man page
isPoly-methods Man page
ktab-class Man page
labels.haploGen Man page
lightseasun Man page
listOrNULL-class Man page
loadingplot Man page
loadingplot.default Man page
loadingplot.glPca Man page
local.rtest Man page
locFac Man page
locFac,genind-method Man page
locFac,gen-method Man page
locFac,genpop-method Man page
locNames Man page
locNames<- Man page
locNames<-,genind-method Man page
locNames,genind-method Man page
locNames<-,genlight-method Man page
locNames,genlight-method Man page
locNames<-,gen-method Man page
locNames,gen-method Man page
locNames<-,genpop-method Man page
locNames,genpop-method Man page
makefreq Man page
makefreq,genind-method Man page
makefreq,genind-methods Man page
makefreq,genpop-method Man page
makefreq,genpop-methods Man page
microbov Man page
minorAllele Man page
monmonier Man page
nAll Man page
nAll,genind-method Man page
nAll,gen-method Man page
nAll,genpop-method Man page
names,genind-method Man page
names,genlight-method Man page
names,genpop-method Man page
names,SNPbin-method Man page
nameStrata Man page
nameStrata<- Man page
nameStrata<-,genind-method Man page
nameStrata,genind-method Man page
nameStrata<-,genlight-method Man page
nameStrata,genlight-method Man page
nancycats Man page
NA.posi Man page
NA.posi,genlight-method Man page
NA.posi,SNPbin-method Man page
nInd Man page
nInd,genind-method Man page
nInd,genlight-method Man page
nLoc Man page
nLoc,genind-method Man page
nLoc,genlight-method Man page
nLoc,gen-method Man page
nLoc,genpop-method Man page
nLoc,SNPbin-method Man page
nPop Man page
nPop,genind-method Man page
nPop,genlight-method Man page
nPop,genpop-method Man page
num2col Man page
old2new Man page
old2new_genind Man page
old2new_genlight Man page
old2new_genpop Man page
optim.a.score Man page
optimize.monmonier Man page
other Man page
other<- Man page
other<-,genind-method Man page
other,genind-method Man page
other<-,genlight-method Man page
other,genlight-method Man page
other<-,gen-method Man page
other,gen-method Man page
other<-,genpop-method Man page
other,genpop-method Man page
pairDist Man page
pairDist.default Man page
pairDistPlot Man page
pairDistPlot.default Man page
pairDistPlot.dist Man page
pairDistPlot.DNAbin Man page
pairDistPlot.genind Man page
pairDistPlot.matrix Man page
ploidy Man page
ploidy<- Man page
ploidy<-,genind-method Man page
ploidy,genind-method Man page
ploidy<-,genlight-method Man page
ploidy,genlight-method Man page
ploidy<-,genpop-method Man page
ploidy,genpop-method Man page
ploidy<-,SNPbin-method Man page
ploidy,SNPbin-method Man page
plot.genlight Man page
plot,genlight,ANY-method Man page
plot,genlight-method Man page
plot.haploGen Man page
plotHaploGen Man page
plot.monmonier Man page
plot.seqTrack Man page
plotSeqTrack Man page
plot.spca Man page
pop Man page
pop<- Man page
pop<-,genind-method Man page
pop,genind-method Man page
pop<-,genlight-method Man page
pop,genlight-method Man page
pop<-,gen-method Man page
popInfo-class Man page
popNames Man page
popNames<- Man page
popNames<-,genind-method Man page
popNames,genind-method Man page
popNames<-,genlight-method Man page
popNames,genlight-method Man page
popNames<-,genpop-method Man page
popNames,genpop-method Man page
position Man page
position<- Man page
position<-,genlight-method Man page
position,genlight-method Man page
predict.dapc Man page
print.dapc Man page
print,genind-method Man page
print.genindSummary Man page
print,genindSummary-method Man page
print.genpopSummary Man page
print,genpopSummary-method Man page
print.glPca Man page
print.haploGen Man page
print.monmonier Man page
print.spca Man page
propShared Man page
propTyped Man page
propTyped,genind-method Man page
propTyped,genpop-method Man page
propTyped-methods Man page
rbind.genlight Man page
.readExt Man page
read.fstat Man page
read.genepop Man page
read.genetix Man page
read.plink Man page
read.PLINK Man page
read.snp Man page
read.structure Man page
redpal Man page
repool Man page
.rmspaces Man page
rupica Man page
sample.haploGen Man page
scaleGen Man page
scaleGen,genind-method Man page
scaleGen,genpop-method Man page
scaleGen-methods Man page
scatter.dapc Man page
scatter.glPca Man page
screeplot.spca Man page
seasun Man page
selPopSize Man page
selPopSize,ANY-method Man page
selPopSize,genind-method Man page
selPopSize-methods Man page
seploc Man page
seploc,ANY-method Man page
seploc,genind-method Man page
seploc,genlight-method Man page
seploc,genpop-method Man page
seploc-methods Man page
seppop Man page
seppop,ANY-method Man page
seppop,genind-method Man page
seppop,genlight-method Man page
seppop-methods Man page
seqTrack Man page
seqTrack-class Man page
seqTrack.default Man page
seqTrack.haploGen Man page
seqTrack.matrix Man page
setPop Man page
setPop<- Man page
setPop<-,genind-method Man page
setPop,genind-method Man page
setPop<-,genlight-method Man page
setPop,genlight-method Man page
show,genind-method Man page
show,genlight-method Man page
show,genpop-method Man page
show,SNPbin-method Man page
sim2pop Man page
SNPbin Man page
[,SNPbin,ANY,ANY,ANY-method Man page
[,SNPbin,ANY,ANY-method Man page
SNPbin-class Man page
,SNPbin-method Man page
[,SNPbin-method Man page
$<-,SNPbin-method Man page
$,SNPbin-method Man page
snpposi.plot Man page
snpposi.plot.DNAbin Man page
snpposi.plot.integer Man page
snpposi.plot.numeric Man page
snpposi.test Man page
snpposi.test.DNAbin Man page
snpposi.test.integer Man page
snpposi.test.numeric Man page
spca Man page
spcaIllus Man page
spectral Man page
splitStrata Man page
splitStrata<- Man page
splitStrata<-,genind-method Man page
splitStrata,genind-method Man page
splitStrata<-,genlight-method Man page
splitStrata,genlight-method Man page
strata Man page
strata<- Man page
strata<-,genind-method Man page
strata,genind-method Man page
strata<-,genlight-method Man page
strata,genlight-method Man page
summary.dapc Man page
summary,genind-method Man page
summary,genpop-method Man page
summary.spca Man page
tab Man page
tab,genind-method Man page
tab,genind-methods Man page
tab,genpop-method Man page
tab,genpop-methods Man page
transp Man page
truenames Man page
truenames,ANY-method Man page
truenames,genind-method Man page
truenames,genpop-method Man page
truenames-methods Man page
usflu Man page
USflu Man page
usflu.fasta Man page
USflu.fasta Man page
.valid.genind Man page
wasp Man page
xvalDapc Man page Man page
xvalDapc.matrix Man page


inst/dapcServer/ui.R inst/dapcServer/server.R
tests/testthat/test-seppop.R tests/testthat/test-prop.R tests/testthat/test_xval.R tests/testthat/test_import.R tests/testthat/test_summary.R tests/testthat/test_repool.R tests/testthat/test_constructors.R tests/testthat/test_accessors.R tests/testthat/test_hierarchy.R tests/testthat/test_subset.R tests/testthat/test_genlight.R
R/classes.R R/glHandle.R R/scale.R R/glPlot.R R/dapc.R R/spca.rtests.R R/minorAllele.R R/orthobasis.R R/basicMethods.R R/makefreq.R R/accessors.R R/handling.R R/snpzip.R R/xvalDapc.R R/genind2genpop.R R/simOutbreak.R R/inbreeding.R R/old2new.R R/propTyped.R R/strataMethods.R R/hybridize.R R/chooseCN.R R/PCtest.R R/adegenet.package.R R/import.R R/haploPop.R R/find.clust.R R/sequences.R R/haploGen.R R/gstat.randtest.R R/Hs.R R/export.R R/coords.monmonier.R R/snpposi.R R/setAs.R R/SNPbin.R R/loadingplot.R R/fstat.R R/hierarchyMethods.R R/gengraph.R R/colorplot.R R/mutations.R R/seqTrack.R R/glFunctions.R R/HWE.R R/glSim.R R/servers.R R/auxil.R R/propShared.R R/pairDist.R R/monmonier.R R/datasets.R R/zzz.R R/constructors.R R/spca.R R/dist.genpop.R
man/as-methods.Rd man/spca.Rd man/propShared.Rd man/import2genind.Rd man/haploGen.Rd man/population-methods.Rd man/new.genpop.Rd man/xvalDapc.Rd man/selpopsize.Rd man/SNPbin.Rd man/dist.genpop.Rd man/glPlot.Rd man/spca.rtests.Rd man/microbov.Rd man/colorplot.Rd man/isPoly.Rd man/sim2pop.Rd man/adegenet.package.Rd man/strata-methods.Rd man/snpposi.Rd man/fasta2genlight.Rd man/read.fstat.Rd man/read.genetix.Rd man/HWE.Rd man/genlight.Rd man/web.Rd man/hierarchy-methods.Rd man/rupica.Rd man/spcaIllus.Rd man/coords.monmonier.Rd man/read.PLINK.Rd man/sequences.Rd man/hybridize.Rd man/inbreeding.Rd man/tab.Rd man/gengraph.Rd man/seppop.Rd man/dapcIllus.Rd man/nancycats.Rd man/loadingplot.Rd man/eHGDP.Rd man/as.genlight.Rd man/monmonier.Rd man/new.genind.Rd man/Hs.test.Rd man/chooseCN.Rd man/ascore.Rd man/glPca.Rd man/old2new.Rd man/genind.Rd man/makefreq.Rd man/virClasses.Rd man/glSim.Rd man/as.SNPbin.Rd man/fasta2DNAbin.Rd man/seqTrack.Rd man/mutations.Rd man/read.snp.Rd man/auxil.Rd man/repool.Rd man/propTyped.Rd man/servers.Rd man/seploc.Rd man/glAux.Rd man/dapc.Rd man/scaleGen.Rd man/Hs.Rd
man/genind2df.Rd man/genind2genpop.Rd man/truenames.Rd man/H3N2.Rd man/read.genepop.Rd man/read.structure.Rd man/find.clusters.Rd man/genpop.Rd man/minorAllele.Rd man/accessors.Rd man/pairDist.Rd man/dapcGraphics.Rd man/df2genind.Rd
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