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

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.

Author
Tatsiana Khamiakova
Date of publication
2014-11-27 15:39:29
Maintainer
Tatsiana Khamiakova <tatsiana.khamiakova@uhasselt.be>
License
GPL (>= 2)
Version
1.1

View on R-Forge

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

Files in this package

superbiclust/DESCRIPTION
superbiclust/NAMESPACE
superbiclust/R
superbiclust/R/HCLtree.R
superbiclust/R/biclustData-class.R
superbiclust/R/getStats.R
superbiclust/R/plotTree.R
superbiclust/R/similarity.R
superbiclust/man
superbiclust/man/BiclustSet-class.Rd
superbiclust/man/BiclustSet-methods.Rd
superbiclust/man/HCLtree.Rd
superbiclust/man/biclustSim-package.Rd
superbiclust/man/combine.Rd
superbiclust/man/getStats.Rd
superbiclust/man/jaccardMat.Rd
superbiclust/man/kulczynskiMat.Rd
superbiclust/man/ochiaiMat.Rd
superbiclust/man/plotProfilesAcrossAllsamples.Rd
superbiclust/man/plotProfileswithinBicluster.Rd
superbiclust/man/plotSuper.Rd
superbiclust/man/plotSuperAll.Rd
superbiclust/man/sensitivityMat.Rd
superbiclust/man/similarity.Rd
superbiclust/man/sorensenMat.Rd
superbiclust/man/specificityMat.Rd