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 |