Exploratory Analysis of Genetic and Genomic Data


[Up] [Top]

Documentation for package ‘adegenet’ version 2.1.3

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 BIC
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