accessors | Accessors for adegenet objects |
adegenet.package | The adegenet package |
AICc | Compute Akaike Information Criterion for small samples (AICc)... |
AIC.snapclust | Compute Akaike Information Criterion (AIC) for snapclust |
ascore | Compute and optimize a-score for Discriminant Analysis of... |
as.genlight | Conversion to class "genlight" |
as-methods | Converting genind/genpop objects to other classes |
as.SNPbin | Conversion to class "SNPbin" |
auxil | Auxiliary functions for adegenet |
BIC.snapclust | Compute Bayesian Information Criterion (BIC) for snapclust |
chooseCN | Function to choose a connection network |
colorplot | Represents a cloud of points with colors |
compoplot | Genotype composition plot |
coords.monmonier | Returns original points in results paths of an object of... |
dapc | Discriminant Analysis of Principal Components (DAPC) |
dapcGraphics | Graphics for Discriminant Analysis of Principal Components... |
dapcIllus | Simulated data illustrating the DAPC |
df2genind | Convert a data.frame of allele data to a genind object. |
dist.genpop | Genetic distances between populations |
doc_C_routines | Internal C routines |
eHGDP | Extended HGDP-CEPH dataset |
export_to_mvmapper | Export analysis for mvmapper visualisation |
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 |
gengraph | Genetic transitive graphs |
genind | 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" |
genpop | adegenet formal class (S4) for allele counts in populations |
glAux | Auxiliary functions for genlight objects |
glPca | Principal Component Analysis for genlight objects |
glPlot | Plotting genlight objects |
glSim | Simulation of simple genlight objects |
H3N2 | Seasonal influenza (H3N2) HA segment data |
haploGen | Simulation of genealogies of haplotypes |
hierarchy-methods | Access and manipulate the population hierarchy for genind or... |
Hs | Expected heterozygosity (Hs) |
Hs.test | Test differences in expected heterozygosity (Hs) |
HWE | Hardy-Weinberg Equilibrium test for multilocus data |
hybridize | Function hybridize takes two genind in inputs and generates... |
hybridtoy | Toy hybrid dataset |
import2genind | Importing data from several softwares to a genind object |
inbreeding | Likelihood-based estimation of inbreeding |
isPoly | Assess polymorphism in genind/genpop objects |
KIC | Compute Akaike Information Criterion for small samples (AICc)... |
loadingplot | Represents a cloud of points with colors |
makefreq | Compute allelic frequencies |
microbov | Microsatellites genotypes of 15 cattle breeds |
minorAllele | Compute minor allele frequency |
monmonier | Boundary detection using Monmonier algorithm |
mutations | Identify mutations between DNA sequences |
nancycats | Microsatellites genotypes of 237 cats from 17 colonies of... |
new.genind | genind constructor |
new.genpop | genpop constructor |
old2new | Convert objects with obsolete classes into new objects |
pairDist | Pairwise distance plots |
population-methods | Manipulate the population factor of genind objects. |
propShared | Compute proportion of shared alleles |
propTyped | Compute the proportion of typed elements |
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.snp | Reading Single Nucleotide Polymorphism data |
read.structure | Reading data from STRUCTURE |
repool | Pool several genotypes into a single dataset |
rupica | Microsatellites genotypes of 335 chamois (Rupicapra... |
scaleGen | Compute scaled allele frequencies |
selpopsize | Select genotypes of well-represented populations |
seploc | Separate data per locus |
seppop | Separate genotypes per population |
seqTrack | SeqTrack algorithm for reconstructing genealogies |
sequences | Importing data from an alignement of sequences to a genind... |
servers | Web servers for adegenet |
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 AIC, BIC or... |
SNPbin | Formal class "SNPbin" |
snpposi | Analyse the position of polymorphic sites |
snpzip | Identification of structural SNPs |
spca | Spatial principal component analysis |
spcaIllus | Simulated data illustrating the sPCA |
spca_randtest | Monte Carlo test for sPCA |
spca.rtests | Global and local tests |
strata-methods | Access and manipulate the population strata for genind or... |
swallowtails | Microsatellites genotypes of 781 swallowtail butterflies from... |
tab | Access allele counts or frequencies |
truenames | Restore true labels of an object |
virClasses | Virtual classes for adegenet |
web | Functions to access online resources for adegenet |
xvalDapc | Cross-validation for Discriminant Analysis of Principal... |
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