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

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.

AuthorKevin R. Coombes
Date of publication2016-05-10 19:24:02
MaintainerKevin R. Coombes <krc@silicovore.com>
LicenseApache License (== 2.0)
Version3.3.3
http://oompa.r-forge.r-project.org/

View on R-Forge

Functions

aspectHeatmap Man page
BootstrapClusterTest Man page
BootstrapClusterTest-class Man page
cluster3 Man page
ClusterTest Man page
ClusterTest-class Man page
cutHclust Man page
cutKmeans Man page
cutPam Man page
cutRepeatedKmeans Man page
distanceMatrix Man page
GenePCA Man page
GenePCA-class Man page
hclust-class Man page
hist,ClusterTest-method Man page
identify,SamplePCA-method Man page
image,ClusterTest-method Man page
mahalanobisQC Man page
Mosaic Man page
Mosaic-class Man page
PCanova Man page
PCanova-class Man page
pcc Man page
PerturbationClusterTest Man page
PerturbationClusterTest-class Man page
plotColoredClusters Man page
plot,GenePCA,missing-method Man page
plot,Mosaic,missing-method Man page
plot,PCanova,missing-method Man page
plot,SamplePCA,missing-method Man page
pltree,Mosaic-method Man page
pltree,PCanova-method Man page
predict,SamplePCA-method Man page
repeatedKmeans Man page
SamplePCA Man page
SamplePCA-class Man page
screeplot,SamplePCA-method Man page
summary,BootstrapClusterTest-method Man page
summary,ClusterTest-method Man page
summary,Mosaic-method Man page
summary,PCanova-method Man page
summary,PerturbationClusterTest-method Man page
summary,SamplePCA-method Man page
text,SamplePCA-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.