/usr/lib/R/site-library/adegenet/INDEX is in r-cran-adegenet 2.1.1-1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 | $,genind-method Accessors for adegenet objects
.internal_C_routines Internal C routines
AIC.snapclust snapclust's Akaike Information Criterion (AIC)
AICc snapclust's corrected Akaike Information
Criterion (AICc)
BIC.snapclust snapclust's Bayesian Information Criterion
(BIC)
DNAbin2genind Importing data from an alignement of sequences
to a genind object
H3N2 Seasonal influenza (H3N2) HA segment data
HWE.test.genind Hardy-Weinberg Equilibrium test for multilocus
data
Hs Expected heterozygosity (Hs)
Hs.test Test differences in expected heterozygosity
(Hs)
KIC snapclust's Kullback Information Criterion
(KIC)
SNPbin-class Formal class "SNPbin"
a.score Compute and optimize a-score for Discriminant
Analysis of Principal Components (DAPC)
adegenet.package The adegenet package
adegenetServer Web servers for adegenet
adegenetWeb Functions to access online resources for
adegenet
as-method Converting genind/genpop objects to other
classes
as.SNPbin Conversion to class "SNPbin"
as.genlight Conversion to class "genlight"
checkType Auxiliary functions for adegenet
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 class 'monmonier'
dapc Discriminant Analysis of Principal Components
(DAPC)
dapcIllus Simulated data illustrating the DAPC
df2genind Convert a data.frame of allele data to a genind
object.
dist.genpop Genetic distances between populations
eHGDP Extended HGDP-CEPH dataset
export_to_mvmapper Export analysis for mvmapper visualisation
extract.PLINKmap Reading PLINK Single Nucleotide Polymorphism
data
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
findMutations Identify mutations between DNA sequences
gengraph Genetic transitive graphs
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-class Formal class "genlight"
genpop-class adegenet formal class (S4) for allele counts in
populations
glPca Principal Component Analysis for genlight
objects
glPlot Plotting genlight objects
glSim Simulation of simple genlight objects
glSum Auxiliary functions for genlight objects
global.rtest Global and local tests
haploGen Simulation of genealogies of haplotypes
hier Access and manipulate the population hierarchy
for genind or genlight objects.
hybridize Function hybridize takes two genind in inputs
and generates hybrids individuals having one
parent in both objects.
hybridtoy Toy hybrid dataset
import2genind Importing data from several softwares to a
genind object
inbreeding Likelihood-based estimation of inbreeding
indInfo-class Virtual classes for adegenet
initialize,genind-method
genind constructor
initialize,genpop-method
genpop constructor
isPoly-methods Assess polymorphism in genind/genpop objects
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
nancycats Microsatellites genotypes of 237 cats from 17
colonies of Nancy (France)
old2new_genind Convert objects with obsolete classes into new
objects
pairDistPlot Pairwise distance plots
propShared Compute proportion of shared alleles
propTyped-methods 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.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 rupicapra) from the Bauges mountains
(France)
scaleGen Compute scaled allele frequencies
scatter.dapc Graphics for Discriminant Analysis of Principal
Components (DAPC)
selPopSize Select genotypes of well-represented
populations
seploc Separate data per locus
seppop Separate genotypes per population
seqTrack SeqTrack algorithm for reconstructing
genealogies
setPop Manipulate the population factor of genind
objects.
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
snpposi.plot 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
strata Access and manipulate the population strata for
genind or genlight objects.
tab Access allele counts or frequencies
truenames Restore true labels of an object
xvalDapc Cross-validation for Discriminant Analysis of
Principal Components (DAPC)
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