superbiclust: Generating Robust Biclusters from a Bicluster Set (Ensemble Biclustering)
Version 1.1

Biclusters are submatrices in the data matrix which satisfy certain conditions of homogeneity. Package contains functions for generating robust biclusters with respect to the initialization parameters for a given bicluster solution contained in a bicluster set in data, the procedure is also known as ensemble biclustering. The set of biclusters is evaluated based on the similarity of its elements (the overlap), and afterwards the hierarchical tree is constructed to obtain cut-off points for the classes of robust biclusters. The result is a number of robust (or super) biclusters with none or low overlap.

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AuthorTatsiana Khamiakova
Date of publication2014-11-27 15:39:29
MaintainerTatsiana Khamiakova <tatsiana.khamiakova@uhasselt.be>
LicenseGPL (>= 2)
Version1.1
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("superbiclust", repos="http://R-Forge.R-project.org")

Man pages

BiclustSet-class: Class 'BiclustSet'
BiclustSet-methods: Constructor of BiclustSet object
biclustSim-package: generating robust biclusters form the set of biclusters
combine: Combine two Biclust objects into one
getStats: Get frequency statistic for the columns and rows membership
HCLtree: Hierarchical structure of bicluster output
jaccardMat: Jaccard similarity Matrix for bicluster output
kulczynskiMat: Kulczynski similarity Matrix for bicluster output
ochiaiMat: Ochiai similarity Matrix for bicluster output
plotProfilesAcrossAllsamples: Plot Gene Expression Profiles Across All Samples of the...
plotProfileswithinBicluster: Plot Gene Expression Profiles within a (Core) Bicluster
plotSuper: Plot gene profiles within biclusters
plotSuperAll: Plot gene profiles for all samples in the data
sensitivityMat: Sensitivity Matrix for bicluster output
similarity: Similarity Matrix for bicluster output
sorensenMat: Sorensen similarity Matrix for bicluster output
specificityMat: Specificity Matrix for bicluster output

Functions

BiclustSet Man page Source code
BiclustSet,ANY-method Man page
BiclustSet,Biclust-method Man page
BiclustSet,Factorization-method Man page
BiclustSet,list-method Man page
BiclustSet-class Man page
BiclustSet-methods Man page
HCLtree Man page Source code
combine Man page Source code
getStats Man page Source code
jaccardMat Man page Source code
kulczynskiMat Man page Source code
ochiaiMat Man page Source code
plotProfilesAcrossAllSamples Man page Source code
plotProfilesWithinBicluster Man page Source code
plotSuper Man page Source code
plotSuperAll Man page Source code
sensitivityMat Man page Source code
show,BiclustSet-method Man page
similarity Man page Source code
sorensenMat Man page Source code
specificityMat Man page Source code
summary,BiclustSet-method Man page
superbiclust Man page
superbiclust-package Man page

Files

DESCRIPTION
NAMESPACE
R
R/HCLtree.R
R/biclustData-class.R
R/getStats.R
R/plotTree.R
R/similarity.R
man
man/BiclustSet-class.Rd
man/BiclustSet-methods.Rd
man/HCLtree.Rd
man/biclustSim-package.Rd
man/combine.Rd
man/getStats.Rd
man/jaccardMat.Rd
man/kulczynskiMat.Rd
man/ochiaiMat.Rd
man/plotProfilesAcrossAllsamples.Rd
man/plotProfileswithinBicluster.Rd
man/plotSuper.Rd
man/plotSuperAll.Rd
man/sensitivityMat.Rd
man/similarity.Rd
man/sorensenMat.Rd
man/specificityMat.Rd
superbiclust documentation built on May 21, 2017, 4:16 a.m.