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superbiclust (version 1.2)

Generating Robust Biclusters from a Bicluster Set (Ensemble Biclustering)

Description

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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Install

install.packages('superbiclust')

Monthly Downloads

452

Version

1.2

License

GPL (>= 2)

Last Published

May 28th, 2021

Functions in superbiclust (1.2)

similarity

Similarity Matrix for bicluster output
sensitivityMat

Sensitivity Matrix for bicluster output
plotSuperAll

Plot gene profiles for all samples in the data
combine

Combine two Biclust objects into one
getStats

Get frequency statistic for the columns and rows membership
sorensenMat

Sorensen similarity Matrix for bicluster output
specificityMat

Specificity Matrix for bicluster output
jaccardMat

Jaccard similarity Matrix for bicluster output
kulczynskiMat

Kulczynski similarity Matrix for bicluster output
superbiclust-package

generating robust biclusters form the set of biclusters
HCLtree

Hierarchical structure of bicluster output
plotProfilesWithinBicluster

Plot Gene Expression Profiles within a (Core) Bicluster
plotSuper

Plot gene profiles within biclusters
plotProfilesAcrossAllSamples

Plot Gene Expression Profiles Across All Samples of the Original Data
ochiaiMat

Ochiai similarity Matrix for bicluster output
BiclustSet-class

Class BiclustSet
BiclustSet-methods

Constructor of BiclustSet object