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


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Documentation for package ‘adegenet’ version 1.1-2

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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
.genlab Utilities functions for adegenet
.readExt Utilities functions for adegenet
.rmspaces Utilities functions for adegenet
.valid.genind adegenet formal class (S4) for individual genotypes
adegenet The adegenet package
adegenetWeb Utilities functions for adegenet
as.genind genind constructor
as.genpop genpop constructor
callOrNULL-class Virtual classes for adegenet
charOrNULL-class Virtual classes for adegenet
chooseCN Function to choose a connection network
coords.monmonier Returns original points in results paths of an object of class 'monmonier'
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
factorOrNULL-class Virtual classes for adegenet
fstat F statistics for genind objects
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
global.rtest Global and local tests
gstat.randtest Goudet's G-statistic Monte Carlo test for genind object
HWE.test.genind Hardy-Weinberg Equilibrium test for multilocus data
hybridize Simulated hybridization between two samples of populations
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
listOrNULL-class Virtual classes for adegenet
local.rtest Global and local tests
makefreq Function to generate allelic frequencies
microbov Microsatellites genotypes of 15 cattle breeds
monmonier Boundary detection using Monmonier algorithm
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)
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
plot.monmonier Boundary detection using Monmonier algorithm
plot.spca Spatial principal component analysis
popInfo-class Virtual classes for adegenet
print,genind-method adegenet formal class (S4) for individual genotypes
print.monmonier Boundary detection using Monmonier algorithm
print.spca Spatial principal component analysis
propShared Compute proportion of shared alleles
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 the same dataset
screeplot.spca Spatial principal component analysis
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
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.spca Spatial principal component analysis
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
[,genind-method Accessors for adegenet objects
[,genpop-method Accessors for adegenet objects