| ClusterJudge-package {ClusterJudge} | R Documentation |
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.
The DESCRIPTION file:
| Package: | ClusterJudge |
| Type: | Package |
| Title: | Judging Quality of Clustering Methods using Mutual Information |
| Version: | 1.4.0 |
| Date: | 2017-02-15 |
| Author: | Adrian Pasculescu |
| Maintainer: | Adrian Pasculescu <pasculescu@lunenfeld.ca> |
| 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 (>= 3.4), 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_8 |
| git_last_commit: | f107994 |
| git_last_commit_date: | 2018-10-30 |
| Date/Publication: | 2018-10-30 |
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.
Adrian Pasculescu
Maintainer: Adrian Pasculescu <pasculescu@lunenfeld.ca>
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.