clusternomics: Integrative Clustering for Heterogeneous Biomedical Datasets
Version 0.1.1

Integrative context-dependent clustering for heterogeneous biomedical datasets. Identifies local clustering structures in related datasets, and a global clusters that exist across the datasets.

AuthorEvelina Gabasova
Date of publication2017-03-14 15:13:04
MaintainerEvelina Gabasova <egabasova@gmail.com>
LicenseMIT + file LICENSE
Version0.1.1
URL https://github.com/evelinag/clusternomics
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("clusternomics")

Getting started

README.md
Context-dependent clustering with Clusternomics

Popular man pages

clusterSizes: Estimate sizes of clusters from global cluster assignments.
contextCluster: Clusternomics: Context-dependent clustering
empiricalBayesPrior: Fit an empirical Bayes prior to the data
generatePrior: Generate a basic prior distribution for the datasets.
generateTestData_1D: Generate simulated 1D dataset for testing
generateTestData_2D: Generate simulated 2D dataset for testing
numberOfClusters: Estimate number of clusters from global cluster assignments.
See all...

All man pages Function index File listing

Man pages

clusterSizes: Estimate sizes of clusters from global cluster assignments.
coclusteringMatrix: Compute the posterior co-clustering matrix from global...
contextCluster: Clusternomics: Context-dependent clustering
empiricalBayesPrior: Fit an empirical Bayes prior to the data
generatePrior: Generate a basic prior distribution for the datasets.
generateTestData_1D: Generate simulated 1D dataset for testing
generateTestData_2D: Generate simulated 2D dataset for testing
numberOfClusters: Estimate number of clusters from global cluster assignments.

Functions

clusterSizes Man page Source code
coclusteringMatrix Man page Source code
computeDIC Source code
contextCluster Man page Source code
createDataStats Source code
createGibbsState Source code
empiricalBayesPrior Man page Source code
generateMapping Source code
generatePrior Man page Source code
generateTestData_1D Man page Source code
generateTestData_2D Man page Source code
getClustersAssignments Source code
getContextClusterMarginals Source code
getContextClusterMarginals_diagNormal Source code
getDataStatistics Source code
getDataStatistics_diagNormal Source code
getGlobalClusterStats Source code
getGlobalClusterStats_diagNormal Source code
getGlobalClusters Source code
getLogliksForContextCluster Source code
getLogliksForGlobalCluster Source code
getMCMCSamples Source code
getMarginal Source code
getParams_diagNormal Source code
gibbsSampleContextK Source code
gibbsSampleZ Source code
initContextClusterStatistics Source code
initContextClusterStatistics_diagNormal Source code
initGlobalClusterStatistics Source code
initGlobalClusterStatistics_diagNormal Source code
logJoint Source code
logK Source code
logZ Source code
logsumexp Source code
marginal_diagNormal Source code
normalizeProbs Source code
numberOfClusters Man page Source code
precomputeClusterStatistics Source code
precomputeDataMarginals Source code
precomputeDataStatistics Source code
predictiveLogLik_diagNormal Source code
predictiveLoglik Source code
rep.col Source code
rep.row Source code
sampleCategorical Source code
saveSample Source code
updateContextClusterStats Source code
updateContextClusterStats_diagNormal Source code
updateGlobalClusterStats Source code
updateGlobalClusterStats_diagNormal Source code

Files

inst
inst/doc
inst/doc/using-clusternomics.Rmd
inst/doc/using-clusternomics.html
inst/doc/using-clusternomics.R
tests
tests/testthat.R
tests/testthat
tests/testthat/test.clusternomics.R
tests/testthat/test.clusternomics.globalBehaviour.R
NAMESPACE
R
R/generatePrior.R
R/empiricalBayesPrior.R
R/generateTestData.R
R/clusternomics.R
R/processResults.R
vignettes
vignettes/using-clusternomics.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/numberOfClusters.Rd
man/generateTestData_2D.Rd
man/coclusteringMatrix.Rd
man/contextCluster.Rd
man/generatePrior.Rd
man/empiricalBayesPrior.Rd
man/generateTestData_1D.Rd
man/clusterSizes.Rd
tools
tools/clustering_structure.png
LICENSE
clusternomics documentation built on May 19, 2017, 11:44 a.m.

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