ClassDiscovery: Classes and Methods for "Class Discovery" with Microarrays or Proteomics

Share:

The ClassDiscovery package defines the classes used for "class discovery" problems in the OOMPA project. Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance.

Author
Kevin R. Coombes
Date of publication
2016-05-10 19:24:02
Maintainer
Kevin R. Coombes <krc@silicovore.com>
License
Apache License (== 2.0)
Version
3.3.3
URLs

View on R-Forge

Man pages

cd01-0-distanceMatrix
Distance Matrix Computation
cd02-0-plotColoredClusters
Plot Dendrograms with Color-Coded Labels
cd02-1-cluster3
Cluster a Dataset Three Ways
cd03-0-ClusterTest-class
Class "ClusterTest"
cd03-1-BootstrapClusterTest-class
Class "BootstrapClusterTest"
cd03-2-hclust-class
Class "hclust"
cd03-3-justClusters
Get the List of Classes From A Clustering Algorithm
cd04-0-PerturbationClusterTest-class
The PerturbationClusterTest Class
cd05-0-SamplePCA-class
Class "SamplePCA"
cd05-1-GenePCA-class
Class "GenePCA"
cd06-0-aspectHeatmap
Heatmap with control over the aspect ratio
cd07-0-Mosaic-class
Class "Mosaic"
cd08-0-PCanova-class
Class "PCanova"
cd10-0-maha
Using Mahalanobis Distance and PCA for Quality Control

Files in this package

ClassDiscovery/DESCRIPTION
ClassDiscovery/NAMESPACE
ClassDiscovery/NEWS
ClassDiscovery/R
ClassDiscovery/R/cd00-generics.R
ClassDiscovery/R/cd01-distance.R
ClassDiscovery/R/cd02-cluster.R
ClassDiscovery/R/cd03-bootclust.R
ClassDiscovery/R/cd04-perclust.R
ClassDiscovery/R/cd05-gene-sample-pca.R
ClassDiscovery/R/cd06-heatmap.R
ClassDiscovery/R/cd07-mosiac.R
ClassDiscovery/R/cd08-pcanova.R
ClassDiscovery/TODO
ClassDiscovery/build
ClassDiscovery/build/vignette.rds
ClassDiscovery/inst
ClassDiscovery/inst/doc
ClassDiscovery/inst/doc/maha-test.R
ClassDiscovery/inst/doc/maha-test.Rnw
ClassDiscovery/inst/doc/maha-test.pdf
ClassDiscovery/inst/doc/oompa-cd.R
ClassDiscovery/inst/doc/oompa-cd.Rnw
ClassDiscovery/inst/doc/oompa-cd.pdf
ClassDiscovery/man
ClassDiscovery/man/cd01-0-distanceMatrix.Rd
ClassDiscovery/man/cd02-0-plotColoredClusters.Rd
ClassDiscovery/man/cd02-1-cluster3.Rd
ClassDiscovery/man/cd03-0-ClusterTest-class.Rd
ClassDiscovery/man/cd03-1-BootstrapClusterTest-class.Rd
ClassDiscovery/man/cd03-2-hclust-class.Rd
ClassDiscovery/man/cd03-3-justClusters.Rd
ClassDiscovery/man/cd04-0-PerturbationClusterTest-class.Rd
ClassDiscovery/man/cd05-0-SamplePCA-class.Rd
ClassDiscovery/man/cd05-1-GenePCA-class.Rd
ClassDiscovery/man/cd06-0-aspectHeatmap.Rd
ClassDiscovery/man/cd07-0-Mosaic-class.Rd
ClassDiscovery/man/cd08-0-PCanova-class.Rd
ClassDiscovery/man/cd10-0-maha.Rd
ClassDiscovery/tests
ClassDiscovery/tests/exprSet-example.R
ClassDiscovery/tests/exprSet-example.Rout.save
ClassDiscovery/tests/test00-color.R
ClassDiscovery/tests/test00-color.Rout.save
ClassDiscovery/tests/test01-distance.R
ClassDiscovery/tests/test01-distance.Rout.save
ClassDiscovery/tests/test02-cluster.R
ClassDiscovery/tests/test02-cluster.Rout.save
ClassDiscovery/tests/test02.1-just.R
ClassDiscovery/tests/test02.1-just.Rout.save
ClassDiscovery/tests/test03-boot.R
ClassDiscovery/tests/test03-boot.Rout.save
ClassDiscovery/tests/test04-perturb.R
ClassDiscovery/tests/test04-perturb.Rout.save
ClassDiscovery/tests/test04.1-gpca.R
ClassDiscovery/tests/test04.1-gpca.Rout.save
ClassDiscovery/tests/test05-spca.R
ClassDiscovery/tests/test05-spca.Rout.save
ClassDiscovery/tests/test06-mosaic.R
ClassDiscovery/tests/test06-mosaic.Rout.save
ClassDiscovery/tests/test07-pcanova.R
ClassDiscovery/tests/test07-pcanova.Rout.save
ClassDiscovery/vignettes
ClassDiscovery/vignettes/maha-test.Rnw
ClassDiscovery/vignettes/oompa-cd.Rnw