Exploratory Analysis of Genetic and Genomic Data

---

Documentation for package ‘adegenet’ version 2.1.11

• DESCRIPTION file.

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

adegenet-package

The adegenet package

-- 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
.render.server.info	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