# adegenet: a R package for the multivariate analysis of genetic markers.

## Documentation for package ‘adegenet’ version 1.2-5

## Help Pages

A C D E F G H I K L M N O P R S T misc

## -- --

adegenet-package | The adegenet package

## -- --

$,genind-method | Accessors for adegenet objects
$,genpop-method | Accessors for adegenet objects
$<-,genind-method | Accessors for adegenet objects
$<-,genpop-method | Accessors for adegenet objects
.find.sub.clusters | find.cluster: cluster identification using successive K-means
.genlab | Utilities functions for adegenet
.readExt | Utilities functions for adegenet
.rmspaces | Utilities functions for adegenet
.valid.genind | adegenet formal class (S4) for individual genotypes

## -- A --

adegenet | The adegenet package
adegenetTutorial | Utilities functions for adegenet
adegenetWeb | Utilities functions for adegenet
as,genind,data.frame-method | Converting genind/genpop objects to other classes
as,genind,genpop-method | Converting genind/genpop objects to other classes
as,genind,ktab-method | Converting genind/genpop objects to other classes
as,genind,matrix-method | Converting genind/genpop objects to other classes
as,genpop,data.frame-method | Converting genind/genpop objects to other classes
as,genpop,ktab-method | Converting genind/genpop objects to other classes
as,genpop,matrix-method | Converting genind/genpop objects to other classes
as,haploGen,graphNEL-method | Simulation of genealogies of haplotypes
as,seqTrack,graphNEL-method | SeqTrack algorithm for reconstructing genealogies
as-method | Converting genind/genpop objects to other classes
as.data.frame.genind | Converting genind/genpop objects to other classes
as.data.frame.genpop | Converting genind/genpop objects to other classes
as.genind | genind constructor
as.genpop | genpop constructor
as.genpop.genind | Converting genind/genpop objects to other classes
as.ktab.genind | Converting genind/genpop objects to other classes
as.ktab.genpop | Converting genind/genpop objects to other classes
as.matrix.genind | Converting genind/genpop objects to other classes
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
assignplot | Discriminant Analysis of Principal Components (DAPC)

## -- C --

callOrNULL-class | Virtual classes for adegenet
charOrNULL-class | Virtual classes for adegenet
checkType | Utilities functions for adegenet
chooseCN | Function to choose a connection network
coerce,genind,data.frame-method | Converting genind/genpop objects to other classes
coerce,genind,genpop-method | Converting genind/genpop objects to other classes
coerce,genind,ktab-method | Converting genind/genpop objects to other classes
coerce,genind,matrix-method | Converting genind/genpop objects to other classes
coerce,genpop,data.frame-method | Converting genind/genpop objects to other classes
coerce,genpop,ktab-method | Converting genind/genpop objects to other classes
coerce,genpop,matrix-method | Converting genind/genpop objects to other classes
coerce,haploGen,graphNEL-method | Simulation of genealogies of haplotypes
coerce,seqTrack,graphNEL-method | SeqTrack algorithm for reconstructing genealogies
colorplot | Represents a cloud of points with colors
colorplot.default | Represents a cloud of points with colors
colorplot.spca | Spatial principal component analysis
coords.monmonier | Returns original points in results paths of an object of class 'monmonier'

## -- D --

dapc | Discriminant Analysis of Principal Components (DAPC)
dapc.data.frame | Discriminant Analysis of Principal Components (DAPC)
dapc.genind | Discriminant Analysis of Principal Components (DAPC)
dapc.matrix | Discriminant Analysis of Principal Components (DAPC)
dapcIllus | Simulated data illustrating the DAPC
df2genind | Convert a data.frame of genotypes to a genind object, and conversely.
dist,genpop,ANY,ANY,ANY,missing-method | adegenet formal class (S4) for allele counts in populations
dist.genpop | Genetic distances between populations
dist.haploPop | Simulation of populations of haplotypes
DNAbin2genind | Importing data from an alignement of sequences to a genind object

## -- E --

eHGDP | Extended HGDP-CEPH dataset

## -- F --

factorOrNULL-class | Virtual classes for adegenet
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.matrix | find.cluster: cluster identification using successive K-means
fstat | F statistics for genind objects

## -- G --

gen-class | Virtual classes for adegenet
genind | genind constructor
genind-class | adegenet formal class (S4) for individual genotypes
genind-methods | genind constructor
genind2df | Convert a data.frame of genotypes to a genind object, and conversely.
genind2genotype | Conversion functions from adegenet to other R packages
genind2genpop | Conversion from a genind to a genpop object
genind2hierfstat | Conversion functions from adegenet to other R packages
genpop | genpop constructor
genpop-class | adegenet formal class (S4) for allele counts in populations
genpop-methods | genpop constructor
get.likelihood | SeqTrack algorithm for reconstructing genealogies
get.likelihood.seqTrack | SeqTrack algorithm for reconstructing genealogies
global.rtest | Global and local tests
gstat.randtest | Goudet's G-statistic Monte Carlo test for genind object

## -- H --

H3N2 | Seasonal influenza (H3N2) HA segment data
haploGen | Simulation of genealogies of haplotypes
haploGen-class | Simulation of genealogies of haplotypes
haploPop | Simulation of populations of haplotypes
haploPopDiv | Simulation of populations of haplotypes
Hs | Expected heterozygosity
HWE.test.genind | Hardy-Weinberg Equilibrium test for multilocus data
hybridize | Simulated hybridization between two samples of populations

## -- I --

import2genind | Importing data from several softwares to a genind object
indInfo-class | Virtual classes for adegenet
intOrNum-class | Virtual classes for adegenet
is.genind | genind constructor
is.genpop | genpop constructor
isPoly | Assess polymorphism in genind/genpop objects
isPoly,genind-method | Assess polymorphism in genind/genpop objects
isPoly,genpop-method | Assess polymorphism in genind/genpop objects
isPoly-methods | Assess polymorphism in genind/genpop objects

## -- K --

ktab-class | Converting genind/genpop objects to other classes

## -- L --

labels.haploGen | Simulation of genealogies of haplotypes
listOrNULL-class | Virtual classes for adegenet
loadingplot | Represents a cloud of points with colors
loadingplot.default | Represents a cloud of points with colors
local.rtest | Global and local tests
locNames | Accessors for adegenet objects
locNames,genind-method | Accessors for adegenet objects
locNames,genpop-method | Accessors for adegenet objects

## -- M --

makefreq | Function to generate allelic frequencies
microbov | Microsatellites genotypes of 15 cattle breeds
monmonier | Boundary detection using Monmonier algorithm

## -- N --

na.replace | Replace missing values (NA) from an object
na.replace,genind-method | Replace missing values (NA) from an object
na.replace,genpop-method | Replace missing values (NA) from an object
na.replace-methods | Replace missing values (NA) from an object
names,genind-method | adegenet formal class (S4) for individual genotypes
names,genpop-method | adegenet formal class (S4) for allele counts in populations
nancycats | Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France)
nLoc | Accessors for adegenet objects
nLoc,genind-method | Accessors for adegenet objects
nLoc,genpop-method | Accessors for adegenet objects

## -- O --

old2new | Convert objects with obsolete classe into new objects
old2new,ANY-method | Convert objects with obsolete classe into new objects
old2new,genind-method | Convert objects with obsolete classe into new objects
old2new,genpop-method | Convert objects with obsolete classe into new objects
old2new-methods | Convert objects with obsolete classe into new objects
optimize.monmonier | Boundary detection using Monmonier algorithm

## -- P --

plot.haploPop | Simulation of populations of haplotypes
plot.monmonier | Boundary detection using Monmonier algorithm
plot.spca | Spatial principal component analysis
plotHaploGen | Simulation of genealogies of haplotypes
plotSeqTrack | SeqTrack algorithm for reconstructing genealogies
pop | Accessors for adegenet objects
pop,genind-method | Accessors for adegenet objects
pop<- | Accessors for adegenet objects
pop<-,genind-method | Accessors for adegenet objects
popInfo-class | Virtual classes for adegenet
print,genind-method | adegenet formal class (S4) for individual genotypes
print.dapc | Discriminant Analysis of Principal Components (DAPC)
print.haploGen | Simulation of genealogies of haplotypes
print.haploPop | Simulation of populations 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,genind-method | Compute the proportion of typed elements
propTyped,genpop-method | Compute the proportion of typed elements
propTyped-methods | Compute the proportion of typed elements

## -- R --

read.fstat | Reading data from Fstat
read.genepop | Reading data from Genepop
read.genetix | Reading data from GENETIX
read.structure | Reading data from STRUCTURE
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
sample.haploPop | Simulation of populations of haplotypes
scaleGen | Compute scaled allele frequencies
scaleGen,genind-method | Compute scaled allele frequencies
scaleGen,genpop-method | Compute scaled allele frequencies
scaleGen-methods | Compute scaled allele frequencies
scatter.dapc | Discriminant Analysis of Principal Components (DAPC)
screeplot.spca | Spatial principal component analysis
selPopSize | Select genotypes of well-represented populations
selPopSize,ANY-method | Select genotypes of well-represented populations
selPopSize,genind-method | Select genotypes of well-represented populations
selPopSize-methods | Select genotypes of well-represented populations
seploc | Separate data per locus
seploc,ANY-method | Separate data per locus
seploc,genind-method | Separate data per locus
seploc,genpop-method | Separate data per locus
seploc-methods | Separate data per locus
seppop | Separate genotypes per population
seppop,ANY-method | Separate genotypes per population
seppop,genind-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
show,genind-method | adegenet formal class (S4) for individual genotypes
show,genpop-method | adegenet formal class (S4) for allele counts in populations
sim2pop | Simulated genotypes of two georeferenced populations
spca | Spatial principal component analysis
spcaIllus | Simulated data illustrating the sPCA
summary,genind-method | adegenet formal class (S4) for individual genotypes
summary,genpop-method | adegenet formal class (S4) for allele counts in populations
summary.dapc | Discriminant Analysis of Principal Components (DAPC)
summary.haploPop | Simulation of populations of haplotypes
summary.spca | Spatial principal component analysis

## -- T --

truenames | Restore true labels of an object
truenames,ANY-method | Restore true labels of an object
truenames,genind-method | Restore true labels of an object
truenames,genpop-method | Restore true labels of an object
truenames-methods | Restore true labels of an object

## -- misc --

[,genind-method | Accessors for adegenet objects
[,genpop-method | Accessors for adegenet objects
[.haploGen | Simulation of genealogies of haplotypes