ClusterJudge-package {ClusterJudge} | R Documentation

## Judging Quality of Clustering Methods using Mutual Information

### Description

ClusterJudge implements the functions, examples and other software published as an algorithm by Gibbons, FD and Roth FP. The article is called "Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation" and it appeared in Genome Research, vol. 12, pp1574-1581 (2002). See package?ClusterJudge for an overview.

### Details

The DESCRIPTION file:

Package: | ClusterJudge
Type: | Package
Title: | Judging Quality of Clustering Methods using Mutual Information
Version: | 1.16.0
Date: | 2021-03-03
Author: | Adrian Pasculescu
Maintainer: | Adrian Pasculescu <a.pasculescu@gmail.com>
Description: | ClusterJudge implements the functions, examples and other software published as an algorithm by Gibbons, FD and Roth FP. The article is called "Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation" and it appeared in Genome Research, vol. 12, pp1574-1581 (2002). See package?ClusterJudge for an overview.
Depends: | R (>= 3.6), stats, utils, graphics, infotheo, lattice, latticeExtra, httr, jsonlite
Suggests: | yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt
License: | Artistic-2.0
biocViews: | Software, StatisticalMethod, Clustering, GeneExpression, GO
LazyLoad: | yes
LazyData: | yes
VignetteBuilder: | knitr
git_url: | https://git.bioconductor.org/packages/ClusterJudge
git_branch: | RELEASE_3_14
git_last_commit: | d9af46d
git_last_commit_date: | 2021-10-26
Date/Publication: | 2021-10-26

Index of help topics:

    ClusterJudge-package    Judging Quality of Clustering Methods using
                            Mutual Information
    Yeast.GO.assocs         Gene Ontology attributes associated to Yeast
                            Gene entities
    attribute_mut_inf       calculates the mutual information between each
                            attribute of the entity.attribute pairs
    clusterJudge            judges clustering using an entity.attribute
                            table
    clusterJudge_z_score    calculates the 'cluster judge' z-score
    consolidate_entity_attribute
                            removes the redundant attributes based on the
                            mutual information between attributes
    convert_Yeast_SGDId_2_systematic
                            converts the SGD Gene Id into the systematic
                            name of the gene
    download_Yeast_GO_mapping
                            downloads the Gene Ontology attributes mapped
                            to Yeast genes
    download_Yeast_Go_terms
                            downloads the description of Gene Ontology
                            attributes
    entities_attribute_stats
                            presents basic statistics on the number of
                            entities per attribute
    mi.GO.Yeast             precalculated mutual information between Gene
                            Ontology attributes of Yeast genes
    validate_association    validates the associations between entities and
                            attributes

ClusterJudge is a way to judge the quality of clustering performed elsewhere on some entities. This judgement is based on some additional entitity-attribute information. For example, using Gene Ontology annotated attributes offered by Saccharomyces Genome Database (SGD), it can judge the clusters of Yeast genes (i.e. entities) resulted from experiments related to the mitotic Yeast cell cycle. This is done by evaluating the mutual information between a gene membership in a cluster, and the attributes it possesses.

### Author(s)

Adrian Pasculescu

Maintainer: Adrian Pasculescu <a.pasculescu@gmail.com>

### References

Gibbons, F.D. and Roth F.P., (2002) Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation. Genome Research, vol. 12, pp1574-1581.

Tavazoie, et al. (1999) Systematic determination of genetic network architecture. Nature Genetics, 22, 281-285

Cho, et al. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Molecular Cell,2, 65-73.

Cover,T.M. and Thomas,J.A. 1991. Elements of information theory (ed. D.L. Schilling). Wiley-Interscience,New York.

[Package ClusterJudge version 1.16.0 Index]