QUBICBiclusterSet-class: Class "QUBICBiclusterSet"
In rqubic: Qualitative biclustering algorithm for expression data analysis in R

Description Objects from the Class Slots Methods Author(s) References See Also Examples

Object representing a set of biclusters identified by the QUBIC algorithm. The class structure inherits the Biclust class in the biclust package.

Created by functions parsing the output files of QUBIC command line tool, or functions calling QUBIC algorithm implementations in R.

Not intended to be created manually by end-users. However, interested users are invited to review the source code or use the showClass method to view the construction of the class.

See the class structure of Biclust. The slots Parameter and Info have been filled with lists releveant to the QUBIC algorithm, and all items should be accessed by S4-methods to make sure the consistency.

Svalue: signature(object = "QUBICBiclusterSet", index = "missing"): Return S values of QUBIC biclusters as a vector
Svalue: signature(object = "QUBICBiclusterSet", index = "numeric"): S values of specified bicluster(s) are returned. Index is one or a vector of integers. Non-integers will be coereced.
[: signature(x = "QUBICBiclusterSet", i = "ANY", j = "missing", drop = "missing"): Returning a subset of the current QUBICBiclusterSet.
parameter: signature(object = "Biclust", index = "character"): return an input parameter specified by the parameter name
parameter: signature(object = "Biclust", index = "missing"): return a list of input parameters used by the biclustering algorithm, for example QUBIC
info: signature(object = "Biclust", index = "ANY"): return information of the biclusters. For end-users, specific information accessors should be preferred, for example features, conditions and Svalue
info: signature(object = "Biclust", index = "missing"): return all information of the biclusters in a list. For end-users, specific information accessors should be preferred, for example features, conditions and Svalue
show: signature(object = "QUBICBiclusterSet"): showing method

Jitao David Zhang <jitao_david.zhang@roche.com>

Guojun Li, Qin Ma, Haibao Tang, Andrew H. Paternson and Ying Xu (2009) QUBIC: a qualitative biclustering algorithm for analyses of gene expression data. Nucleic Acids Research, 37:e101

Biclust is the basic block accomodating biclusters identified by the QUBIC algorithm.