R: Exploratory Analysis of Genetic and Genomic Data

# Exploratory Analysis of Genetic and Genomic Data

## Documentation for package ‘adegenet’ version 2.1.7

- DESCRIPTION file.

## Help Pages

A B C D E F G H I K L M N O P R S T U V W X misc

## -- A --

a.score | Compute and optimize a-score for Discriminant Analysis of Principal Components (DAPC)
addStrata | Access and manipulate the population strata for genind or genlight objects.
addStrata-method | Access and manipulate the population strata for genind or genlight objects.
addStrata<- | Access and manipulate the population strata for genind or genlight objects.
addStrata<--method | Access and manipulate the population strata for genind or genlight objects.
adegenet | The adegenet package
adegenet.package | The adegenet package
adegenetIssues | Functions to access online resources for adegenet
adegenetServer | Web servers for adegenet
adegenetTutorial | Functions to access online resources for adegenet
adegenetWeb | Functions to access online resources for adegenet
AIC.snapclust | Compute Akaike Information Criterion (AIC) for snapclust
AICc | Compute Akaike Information Criterion for small samples (AICc) for snapclust
AICc.snapclust | Compute Akaike Information Criterion for small samples (AICc) for snapclust
alignment2genind | Importing data from an alignement of sequences to a genind object
alleles | Accessors for adegenet objects
alleles-method | Accessors for adegenet objects
alleles-method | Formal class "genlight"
alleles<- | Accessors for adegenet objects
alleles<--method | Accessors for adegenet objects
alleles<--method | Formal class "genlight"
any2col | Auxiliary functions for adegenet
as-method | Formal class "SNPbin"
as-method | Converting genind/genpop objects to other classes
as-method | Conversion to class "SNPbin"
as-method | Conversion to class "genlight"
as-method | Formal class "genlight"
as.data.frame.genind | Converting genind/genpop objects to other classes
as.data.frame.genlight | Formal class "genlight"
as.data.frame.genpop | Converting genind/genpop objects to other classes
as.genind | genind constructor
as.genlight | Conversion to class "genlight"
as.genlight-method | Conversion to class "genlight"
as.genpop | genpop constructor
as.genpop.genind | Converting genind/genpop objects to other classes
as.igraph.haploGen | Simulation of genealogies of haplotypes
as.igraph.seqTrack | SeqTrack algorithm for reconstructing genealogies
as.integer.SNPbin | Formal class "SNPbin"
as.ktab.genind | Converting genind/genpop objects to other classes
as.ktab.genpop | Converting genind/genpop objects to other classes
as.lda | Discriminant Analysis of Principal Components (DAPC)
as.lda.dapc | Discriminant Analysis of Principal Components (DAPC)
as.list.genlight | Formal class "genlight"
as.matrix.genind | Converting genind/genpop objects to other classes
as.matrix.genlight | Formal class "genlight"
as.matrix.genpop | Converting genind/genpop objects to other classes
as.POSIXct.haploGen | Simulation of genealogies of haplotypes
as.seqTrack.haploGen | Simulation of genealogies of haplotypes
as.SNPbin | Conversion to class "SNPbin"
as.SNPbin-method | Conversion to class "SNPbin"
assignplot | Graphics for Discriminant Analysis of Principal Components (DAPC)
azur | Auxiliary functions for adegenet

## -- B --

BIC.snapclust | Compute Bayesian Information Criterion (BIC) for snapclust
binIntToBytes | Internal C routines
bluepal | Auxiliary functions for adegenet
bytesToBinInt | Internal C routines
bytesToInt | Internal C routines

## -- C --

c.SNPbin | Formal class "SNPbin"
callOrNULL-class | Virtual classes for adegenet
cbind.genlight | Formal class "genlight"
cbind.SNPbin | Formal class "SNPbin"
charOrNULL-class | Virtual classes for adegenet
CheckAllSeg | Internal C routines
checkType | Auxiliary functions for adegenet
chooseCN | Function to choose a connection network
chr | Formal class "genlight"
chr-method | Formal class "genlight"
chr<- | Formal class "genlight"
chr<--method | Formal class "genlight"
chromosome | Formal class "genlight"
chromosome-method | Formal class "genlight"
chromosome<- | Formal class "genlight"
chromosome<--method | Formal class "genlight"
coerce-method | Formal class "SNPbin"
coerce-method | Converting genind/genpop objects to other classes
coerce-method | Conversion to class "SNPbin"
coerce-method | Conversion to class "genlight"
coerce-method | Formal class "genlight"
colorplot | Represents a cloud of points with colors
colorplot.default | Represents a cloud of points with colors
colorplot.spca | Spatial principal component analysis
compoplot | Genotype composition plot
compoplot.dapc | Genotype composition plot
compoplot.matrix | Genotype composition plot
compoplot.snapclust | Genotype composition plot
coords.monmonier | Returns original points in results paths of an object of class 'monmonier'
corner | Auxiliary functions for adegenet

## -- D --

dapc | Discriminant Analysis of Principal Components (DAPC)
dapc.data.frame | Discriminant Analysis of Principal Components (DAPC)
dapc.dudi | Discriminant Analysis of Principal Components (DAPC)
dapc.genind | Discriminant Analysis of Principal Components (DAPC)
dapc.genlight | Discriminant Analysis of Principal Components (DAPC)
dapc.matrix | Discriminant Analysis of Principal Components (DAPC)
dapcIllus | Simulated data illustrating the DAPC
deepseasun | Auxiliary functions for adegenet
df2genind | Convert a data.frame of allele data to a genind object.
dfOrNULL-class | Virtual classes for adegenet
dim-method | Formal class "genlight"
dist-method | adegenet formal class (S4) for allele counts in populations
dist.genpop | Genetic distances between populations
DNAbin2genind | Importing data from an alignement of sequences to a genind object

## -- E --

eHGDP | Extended HGDP-CEPH dataset
export_to_mvmapper | Export analysis for mvmapper visualisation
export_to_mvmapper.dapc | Export analysis for mvmapper visualisation
export_to_mvmapper.default | Export analysis for mvmapper visualisation
export_to_mvmapper.dudi | Export analysis for mvmapper visualisation
export_to_mvmapper.spca | Export analysis for mvmapper visualisation
extract.PLINKmap | Reading PLINK Single Nucleotide Polymorphism data

## -- F --

fac2col | Auxiliary functions for adegenet
factorOrNULL-class | Virtual classes for adegenet
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
find.clusters.data.frame | find.cluster: cluster identification using successive K-means
find.clusters.genind | find.cluster: cluster identification using successive K-means
find.clusters.genlight | find.cluster: cluster identification using successive K-means
find.clusters.matrix | find.cluster: cluster identification using successive K-means
findMutations | Identify mutations between DNA sequences
findMutations.DNAbin | Identify mutations between DNA sequences
flame | Auxiliary functions for adegenet
formOrNULL-class | Virtual classes for adegenet
funky | Auxiliary functions for adegenet

## -- G --

gen-class | Virtual classes for adegenet
gengraph | Genetic transitive graphs
gengraph.default | Genetic transitive graphs
gengraph.dist | Genetic transitive graphs
gengraph.DNAbin | Genetic transitive graphs
gengraph.genind | Genetic transitive graphs
gengraph.genpop | Genetic transitive graphs
gengraph.matrix | Genetic transitive graphs
genind | genind constructor
genind-class | 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"
genlight-class | Formal class "genlight"
genpop | genpop constructor
genpop-class | adegenet formal class (S4) for allele counts in populations
get.likelihood | SeqTrack algorithm for reconstructing genealogies
get.likelihood.seqTrack | SeqTrack algorithm for reconstructing genealogies
GLdotProd | Internal C routines
glDotProd | Auxiliary functions for genlight objects
glMean | Auxiliary functions for genlight objects
glNA | Auxiliary functions for genlight objects
global.rtest | Global and local tests
glPca | Principal Component Analysis for genlight objects
glPlot | Plotting genlight objects
glSim | Simulation of simple genlight objects
glSum | Auxiliary functions for genlight objects
GLsumFreq | Internal C routines
GLsumInt | Internal C routines
glVar | Auxiliary functions for genlight objects
graphMutations | Identify mutations between DNA sequences
graphMutations.DNAbin | Identify mutations between DNA sequences
greenpal | Auxiliary functions for adegenet
greypal | Auxiliary functions for adegenet

## -- H --

H3N2 | Seasonal influenza (H3N2) HA segment data
haploGen | Simulation of genealogies of haplotypes
haploGen-class | Simulation of genealogies of haplotypes
hier | Access and manipulate the population hierarchy for genind or genlight objects.
hier-method | Access and manipulate the population hierarchy for genind or genlight objects.
hier<- | Access and manipulate the population hierarchy for genind or genlight objects.
hier<--method | Access and manipulate the population hierarchy for genind or genlight objects.
Hs | Expected heterozygosity (Hs)
Hs.test | Test differences in expected heterozygosity (Hs)
HWE.test.genind | Hardy-Weinberg Equilibrium test for multilocus data
hybridize | Function hybridize takes two genind in inputs and generates hybrids individuals having one parent in both objects.
hybridpal | Auxiliary functions for adegenet
hybridtoy | Toy hybrid dataset

## -- I --

import2genind | Importing data from several softwares to a genind object
inbreeding | Likelihood-based estimation of inbreeding
indInfo-class | Virtual classes for adegenet
indNames | Accessors for adegenet objects
indNames-method | Accessors for adegenet objects
indNames-method | Formal class "genlight"
indNames<- | Accessors for adegenet objects
indNames<--method | Accessors for adegenet objects
indNames<--method | Formal class "genlight"
initialize,genind-methods | genind constructor
initialize,genpop-methods | genpop constructor
initialize-method | Formal class "SNPbin"
initialize-method | Formal class "genlight"
initialize-method | genind constructor
initialize-method | genpop constructor
intOrNULL-class | Virtual classes for adegenet
intOrNum-class | Virtual classes for adegenet
is.genind | adegenet formal class (S4) for individual genotypes
is.genpop | adegenet formal class (S4) for allele counts in populations
isPoly | Assess polymorphism in genind/genpop objects
isPoly-method | Assess polymorphism in genind/genpop objects
isPoly-methods | Assess polymorphism in genind/genpop objects

## -- K --

KIC | Compute Akaike Information Criterion for small samples (AICc) for snapclust
KIC.snapclust | Compute Akaike Information Criterion for small samples (AICc) for snapclust
ktab-class | Converting genind/genpop objects to other classes

## -- L --

labels.haploGen | Simulation of genealogies of haplotypes
lightseasun | Auxiliary functions for adegenet
listOrNULL-class | Virtual classes for adegenet
loadingplot | Represents a cloud of points with colors
loadingplot.default | Represents a cloud of points with colors
loadingplot.glPca | Principal Component Analysis for genlight objects
local.rtest | Global and local tests
locFac | Accessors for adegenet objects
locFac-method | Accessors for adegenet objects
locNames | Accessors for adegenet objects
locNames-method | Accessors for adegenet objects
locNames-method | Formal class "genlight"
locNames<- | Accessors for adegenet objects
locNames<--method | Accessors for adegenet objects
locNames<--method | Formal class "genlight"

## -- M --

makefreq | Compute allelic frequencies
makefreq,genind-methods | Compute allelic frequencies
makefreq,genpop-methods | Compute allelic frequencies
makefreq-method | Compute allelic frequencies
makefreq.genind | Compute allelic frequencies
makefreq.genpop | Compute allelic frequencies
microbov | Microsatellites genotypes of 15 cattle breeds
minorAllele | Compute minor allele frequency
monmonier | Boundary detection using Monmonier algorithm

## -- N --

NA.posi | Formal class "genlight"
NA.posi-method | Formal class "SNPbin"
NA.posi-method | Formal class "genlight"
nAll | Accessors for adegenet objects
nAll-method | Accessors for adegenet objects
names-method | Formal class "SNPbin"
names-method | adegenet formal class (S4) for individual genotypes
names-method | Formal class "genlight"
names-method | adegenet formal class (S4) for allele counts in populations
nameStrata | Access and manipulate the population strata for genind or genlight objects.
nameStrata-method | Access and manipulate the population strata for genind or genlight objects.
nameStrata<- | Access and manipulate the population strata for genind or genlight objects.
nameStrata<--method | Access and manipulate the population strata for genind or genlight objects.
nancycats | Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France)
nb_shared_all | Internal C routines
nInd | Accessors for adegenet objects
nInd-method | Accessors for adegenet objects
nInd-method | Formal class "genlight"
nLoc | Accessors for adegenet objects
nLoc-method | Formal class "SNPbin"
nLoc-method | Accessors for adegenet objects
nLoc-method | Formal class "genlight"
nPop | Accessors for adegenet objects
nPop-method | Accessors for adegenet objects
nPop-method | Formal class "genlight"
num2col | Auxiliary functions for adegenet

## -- O --

old2new | Convert objects with obsolete classes into new objects
old2new_genind | Convert objects with obsolete classes into new objects
old2new_genlight | Convert objects with obsolete classes into new objects
old2new_genpop | Convert objects with obsolete classes into new objects
optim.a.score | Compute and optimize a-score for Discriminant Analysis of Principal Components (DAPC)
optimize.monmonier | Boundary detection using Monmonier algorithm
other | Accessors for adegenet objects
other-method | Accessors for adegenet objects
other-method | Formal class "genlight"
other<- | Accessors for adegenet objects
other<--method | Accessors for adegenet objects
other<--method | Formal class "genlight"

## -- P --

pairDist | Pairwise distance plots
pairDist.default | Pairwise distance plots
pairDistPlot | Pairwise distance plots
pairDistPlot.default | Pairwise distance plots
pairDistPlot.dist | Pairwise distance plots
pairDistPlot.DNAbin | Pairwise distance plots
pairDistPlot.genind | Pairwise distance plots
pairDistPlot.matrix | Pairwise distance plots
ploidy | Accessors for adegenet objects
ploidy-method | Formal class "SNPbin"
ploidy-method | Accessors for adegenet objects
ploidy-method | Formal class "genlight"
ploidy<- | Accessors for adegenet objects
ploidy<--method | Formal class "SNPbin"
ploidy<--method | Accessors for adegenet objects
ploidy<--method | Formal class "genlight"
plot-method | Plotting genlight objects
plot.genlight | Plotting genlight objects
plot.haploGen | Simulation of genealogies of haplotypes
plot.monmonier | Boundary detection using Monmonier algorithm
plot.seqTrack | SeqTrack algorithm for reconstructing genealogies
plot.spca | Spatial principal component analysis
plotHaploGen | Simulation of genealogies of haplotypes
plotSeqTrack | SeqTrack algorithm for reconstructing genealogies
pop | Accessors for adegenet objects
pop-method | Accessors for adegenet objects
pop-method | Formal class "genlight"
pop<- | Accessors for adegenet objects
pop<--method | Accessors for adegenet objects
pop<--method | Formal class "genlight"
popInfo-class | Virtual classes for adegenet
popNames | Accessors for adegenet objects
popNames-method | Accessors for adegenet objects
popNames-method | Formal class "genlight"
popNames<- | Accessors for adegenet objects
popNames<--method | Accessors for adegenet objects
popNames<--method | Formal class "genlight"
position | Formal class "genlight"
position-method | Formal class "genlight"
position<- | Formal class "genlight"
position<--method | Formal class "genlight"
predict.dapc | Discriminant Analysis of Principal Components (DAPC)
print-method | adegenet formal class (S4) for individual genotypes
print-method | adegenet formal class (S4) for allele counts in populations
print.dapc | Discriminant Analysis of Principal Components (DAPC)
print.genindSummary | adegenet formal class (S4) for individual genotypes
print.genpopSummary | adegenet formal class (S4) for allele counts in populations
print.glPca | Principal Component Analysis for genlight objects
print.haploGen | Simulation of genealogies of haplotypes
print.monmonier | Boundary detection using Monmonier algorithm
print.spca | Spatial principal component analysis
propShared | Compute proportion of shared alleles
propTyped | Compute the proportion of typed elements
propTyped-method | Compute the proportion of typed elements
propTyped-methods | Compute the proportion of typed elements

## -- R --

rbind.genlight | Formal class "genlight"
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.plink | Reading PLINK Single Nucleotide Polymorphism data
read.snp | Reading Single Nucleotide Polymorphism data
read.structure | Reading data from STRUCTURE
redpal | Auxiliary functions for adegenet
repool | Pool several genotypes into a single dataset
rupica | Microsatellites genotypes of 335 chamois (Rupicapra rupicapra) from the Bauges mountains (France)

## -- S --

sample.haploGen | Simulation of genealogies of haplotypes
scaleGen | Compute scaled allele frequencies
scaleGen-method | Compute scaled allele frequencies
scaleGen-methods | Compute scaled allele frequencies
scatter.dapc | Graphics for Discriminant Analysis of Principal Components (DAPC)
scatter.glPca | Principal Component Analysis for genlight objects
screeplot.spca | Spatial principal component analysis
seasun | Auxiliary functions for adegenet
selPopSize | Select genotypes of well-represented populations
selPopSize-method | Select genotypes of well-represented populations
selPopSize-methods | Select genotypes of well-represented populations
seploc | Separate data per locus
seploc-method | Separate data per locus
seploc-methods | Separate data per locus
seppop | Separate genotypes per population
seppop-method | Separate genotypes per population
seppop-methods | Separate genotypes per population
seqTrack | SeqTrack algorithm for reconstructing genealogies
seqTrack-class | SeqTrack algorithm for reconstructing genealogies
seqTrack.default | SeqTrack algorithm for reconstructing genealogies
seqTrack.haploGen | Simulation of genealogies of haplotypes
seqTrack.matrix | SeqTrack algorithm for reconstructing genealogies
setPop | Manipulate the population factor of genind objects.
setPop-method | Manipulate the population factor of genind objects.
setPop<- | Manipulate the population factor of genind objects.
setPop<--method | Manipulate the population factor of genind objects.
show-method | Formal class "SNPbin"
show-method | adegenet formal class (S4) for individual genotypes
show-method | Formal class "genlight"
show-method | adegenet formal class (S4) for allele counts in populations
showmekittens | When you need a break...
sim2pop | Simulated genotypes of two georeferenced populations
snapclust | Maximum-likelihood genetic clustering using EM algorithm
snapclust.choose.k | Choose the number of clusters for snapclust using AIC, BIC or AICc
SNPbin | Formal class "SNPbin"
SNPbin-class | Formal class "SNPbin"
snpposi.plot | Analyse the position of polymorphic sites
snpposi.plot.DNAbin | Analyse the position of polymorphic sites
snpposi.plot.integer | Analyse the position of polymorphic sites
snpposi.plot.numeric | Analyse the position of polymorphic sites
snpposi.test | Analyse the position of polymorphic sites
snpposi.test.DNAbin | Analyse the position of polymorphic sites
snpposi.test.integer | Analyse the position of polymorphic sites
snpposi.test.numeric | Analyse the position of polymorphic sites
snpzip | Identification of structural SNPs
spca | Spatial principal component analysis
spca.data.frame | Spatial principal component analysis
spca.default | Spatial principal component analysis
spca.genind | Spatial principal component analysis
spca.genpop | Spatial principal component analysis
spca.matrix | Spatial principal component analysis
spcaIllus | Simulated data illustrating the sPCA
spca_randtest | Monte Carlo test for sPCA
spectral | Auxiliary functions for adegenet
splitStrata | Access and manipulate the population strata for genind or genlight objects.
splitStrata-method | Access and manipulate the population strata for genind or genlight objects.
splitStrata<- | Access and manipulate the population strata for genind or genlight objects.
splitStrata<--method | Access and manipulate the population strata for genind or genlight objects.
strata | Access and manipulate the population strata for genind or genlight objects.
strata-method | Access and manipulate the population strata for genind or genlight objects.
strata<- | Access and manipulate the population strata for genind or genlight objects.
strata<--method | Access and manipulate the population strata for genind or genlight objects.
summary-method | adegenet formal class (S4) for individual genotypes
summary-method | adegenet formal class (S4) for allele counts in populations
summary.dapc | Discriminant Analysis of Principal Components (DAPC)
summary.spca | Spatial principal component analysis
swallowtails | Microsatellites genotypes of 781 swallowtail butterflies from 40 populations in Alberta and British Columbia, Canada

## -- T --

tab | Access allele counts or frequencies
tab,genind-methods | Access allele counts or frequencies
tab,genpop-methods | Access allele counts or frequencies
tab-method | Formal class "genlight"
tab-method | Access allele counts or frequencies
tab.genind | Access allele counts or frequencies
tab.genpop | Access allele counts or frequencies
transp | Auxiliary functions for adegenet
truenames | Restore true labels of an object
truenames-method | Restore true labels of an object
truenames-methods | Restore true labels of an object

## -- U --

USflu | Seasonal influenza (H3N2) HA segment data
usflu | Seasonal influenza (H3N2) HA segment data
USflu.fasta | Seasonal influenza (H3N2) HA segment data
usflu.fasta | Seasonal influenza (H3N2) HA segment data

## -- V --

virid | Auxiliary functions for adegenet

## -- W --

wasp | Auxiliary functions for adegenet

## -- X --

xvalDapc | Cross-validation for Discriminant Analysis of Principal Components (DAPC)
xvalDapc.data.frame | Cross-validation for Discriminant Analysis of Principal Components (DAPC)
xvalDapc.default | Cross-validation for Discriminant Analysis of Principal Components (DAPC)
xvalDapc.genind | Cross-validation for Discriminant Analysis of Principal Components (DAPC)
xvalDapc.genlight | Cross-validation for Discriminant Analysis of Principal Components (DAPC)
xvalDapc.matrix | Cross-validation for Discriminant Analysis of Principal Components (DAPC)

## -- misc --

$-method | Formal class "SNPbin"
$-method | Accessors for adegenet objects
$-method | Formal class "genlight"
$<--method | Formal class "SNPbin"
$<--method | Accessors for adegenet objects
$<--method | Formal class "genlight"
.find.sub.clusters | find.cluster: cluster identification using successive K-means
.genlab | Auxiliary functions for adegenet
.internal_C_routines | Internal C routines
.readExt | Auxiliary functions for adegenet
.rmspaces | Auxiliary functions for adegenet
.valid.genind | adegenet formal class (S4) for individual genotypes
[-method | Formal class "SNPbin"
[-method | Accessors for adegenet objects
[-method | Formal class "genlight"
[.haploGen | Simulation of genealogies of haplotypes