adegenet: an R package for the exploratory analysis of genetic and genomic data.


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Documentation for package ‘adegenet’ version 1.3-6

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

adegenet-package The adegenet package

-- A --

a.score Compute and optimize a-score for Discriminant Analysis of Principal Components (DAPC)
adegenet The adegenet package
adegenetWeb Auxiliary functions for adegenet
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"
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)

-- B --

bluepal Auxiliary functions for adegenet

-- 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
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 Graphics for Discriminant Analysis of Principal Components (DAPC)
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 genotypes to a genind object, and conversely.
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
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
FST F statistics for genind objects
fst F statistics for genind objects
fstat F statistics for genind objects
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
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
genlight Formal class "genlight"
genlight-class Formal class "genlight"
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
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
glVar Auxiliary functions for genlight objects
graphMutations Identify mutations between DNA sequences
graphMutations.DNAbin Identify mutations between DNA sequences
greenpal Auxiliary functions for adegenet
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
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
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-method Formal class "SNPbin"
initialize-method Formal class "genlight"
intOrNULL-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-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
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
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 Function to generate allelic frequencies
microbov Microsatellites genotypes of 15 cattle breeds
monmonier Boundary detection using Monmonier algorithm

-- N --

NA.posi Formal class "genlight"
NA.posi-method Formal class "SNPbin"
NA.posi-method Formal class "genlight"
na.replace Replace missing values (NA) from an object
na.replace-method Replace missing values (NA) from an object
na.replace-methods Replace missing values (NA) from an object
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
nancycats Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France)
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"
num2col Auxiliary functions for adegenet

-- O --

old2new Convert objects with obsolete classe into new objects
old2new-method Convert objects with obsolete classe into new objects
old2new-methods Convert objects with obsolete classe 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 --

pairwise.fst F statistics for genind objects
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
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.dapc Discriminant Analysis of Principal Components (DAPC)
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
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
sim2pop Simulated genotypes of two georeferenced populations
SNPbin Formal class "SNPbin"
SNPbin-class Formal class "SNPbin"
spca Spatial principal component analysis
spcaIllus Simulated data illustrating the sPCA
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

-- T --

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

-- 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
.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