COMMUNAL: Robust Selection of Cluster Number K
Version 1.1.0

Facilitates optimal clustering of a data set. Provides a framework to run a wide range of clustering algorithms to determine the optimal number (k) of clusters in the data. Then analyzes the cluster assignments from each clustering algorithm to identify samples that repeatedly classify to the same group. We call these 'core clusters', providing a basis for later class discovery.

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AuthorAlbert Chen [aut, cre], Timothy E Sweeney [aut], Olivier Gevaert [ths]
Date of publication2015-10-12 00:26:16
MaintainerAlbert Chen <acc2015@stanford.edu>
LicenseGPL-2
Version1.1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("COMMUNAL")

Man pages

BRCA.100: Breast Cancer gene expression data.
BRCA.results: TCGA Breast Cancer subset 'clusterRange' output
clusterKeys: Rekey cluster assignments.
clusterRange: Run COMMUNAL over a range of data subsets
COMMUNAL: Run clustering algorithms and evaluate validation metrics.
COMMUNAL-class: Class '"COMMUNAL"'
COMMUNAL-package: COmbined Mapping of Multiple clUsteriNg ALgorithms
examineCounts: Examine algorithm cluster agreement
measureMonotonic: Measure cluster monotonicty within the output from...
plotRange3D: Visualize cluster stability
returnCore: Assign points to core clusters
testAlgsMinSize: Choose Optimal Clustering Algorithms

Functions

BRCA.100 Man page
BRCA.results Man page
COMMUNAL Man page Source code
COMMUNAL-class Man page
COMMUNAL-package Man page
addLayer Source code
cleanClusters Source code
clusCounts Source code
clusterKeys Man page Source code
clusterKeys.internal Source code
clusterRange Man page Source code
count_clusters Source code
examineCounts Man page Source code
findSteepestPeak Source code
flipLevels Source code
gapStat_BootData Source code
genClustMtx Source code
genRow Source code
genTestMtx Source code
getGoodAlgs Man page Source code
getKeys Source code
getNonCorrNonMonoMeasures Man page Source code
getScaledAverages Source code
getValidation Source code
induceError Source code
meas.flip Source code
measuresCorr Man page Source code
monotoneClusterRange Man page Source code
optAlg Source code
plotMeans Source code
plotRange Source code
plotRange3D Man page Source code
reorderMat Source code
returnCore Man page Source code
splitOutDuplicates Source code
swapKeys Source code
testAlgsMinSize Man page Source code

Files

inst
inst/CITATION
inst/tests
inst/tests/unittest.R
inst/doc
inst/doc/COMMUNAL.Rnw
inst/doc/COMMUNAL.R
inst/doc/COMMUNAL.pdf
tests
tests/runTestSuite.R
NAMESPACE
data
data/BRCA.results.RData
data/BRCA.100.RData
R
R/extract_core.R
R/plot_range_3d.R
R/communal.R
R/test_range.R
vignettes
vignettes/COMMUNAL.Rnw
vignettes/COMMUNAL-concordance.tex
vignettes/snapshot.png
vignettes/framed.sty
MD5
build
build/vignette.rds
DESCRIPTION
man
man/measureMonotonic.Rd
man/COMMUNAL.Rd
man/plotRange3D.Rd
man/COMMUNAL-class.Rd
man/clusterKeys.Rd
man/clusterRange.Rd
man/BRCA.results.Rd
man/COMMUNAL-package.Rd
man/testAlgsMinSize.Rd
man/returnCore.Rd
man/BRCA.100.Rd
man/examineCounts.Rd
COMMUNAL documentation built on May 19, 2017, 4:29 p.m.