COMMUNAL: Robust Selection of Cluster Number K

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.

Author
Albert Chen [aut, cre], Timothy E Sweeney [aut], Olivier Gevaert [ths]
Date of publication
2015-10-12 00:26:16
Maintainer
Albert Chen <acc2015@stanford.edu>
License
GPL-2
Version
1.1.0

View on CRAN

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

Files in this package

COMMUNAL
COMMUNAL/inst
COMMUNAL/inst/CITATION
COMMUNAL/inst/tests
COMMUNAL/inst/tests/unittest.R
COMMUNAL/inst/doc
COMMUNAL/inst/doc/COMMUNAL.Rnw
COMMUNAL/inst/doc/COMMUNAL.R
COMMUNAL/inst/doc/COMMUNAL.pdf
COMMUNAL/tests
COMMUNAL/tests/runTestSuite.R
COMMUNAL/NAMESPACE
COMMUNAL/data
COMMUNAL/data/BRCA.results.RData
COMMUNAL/data/BRCA.100.RData
COMMUNAL/R
COMMUNAL/R/extract_core.R
COMMUNAL/R/plot_range_3d.R
COMMUNAL/R/communal.R
COMMUNAL/R/test_range.R
COMMUNAL/vignettes
COMMUNAL/vignettes/COMMUNAL.Rnw
COMMUNAL/vignettes/COMMUNAL-concordance.tex
COMMUNAL/vignettes/snapshot.png
COMMUNAL/vignettes/framed.sty
COMMUNAL/MD5
COMMUNAL/build
COMMUNAL/build/vignette.rds
COMMUNAL/DESCRIPTION
COMMUNAL/man
COMMUNAL/man/measureMonotonic.Rd
COMMUNAL/man/COMMUNAL.Rd
COMMUNAL/man/plotRange3D.Rd
COMMUNAL/man/COMMUNAL-class.Rd
COMMUNAL/man/clusterKeys.Rd
COMMUNAL/man/clusterRange.Rd
COMMUNAL/man/BRCA.results.Rd
COMMUNAL/man/COMMUNAL-package.Rd
COMMUNAL/man/testAlgsMinSize.Rd
COMMUNAL/man/returnCore.Rd
COMMUNAL/man/BRCA.100.Rd
COMMUNAL/man/examineCounts.Rd