CLEAN.Mm-package: Data package to provide functional categories to the CLEAN...

In uc-bd2k/CLEAN.Mm: Data package to provide functional categories to the CLEAN package.

Data package to provide functional categories to the CLEAN package.

Description

Provide functional specific to Mus musculus to the CLEAN package. GO : Gene Ontolgy categories derived from packages GO.db and org.Mm.eg.db chrLoc: Cytogenetic bands, derived from the org.Mm.eg.db package geneRIFs: Keyword based text search of cancer related gene RIFs. Derived from NCBI gene RIFs (Gene Reference Into Function, websites: http://www.ncbi.nlm.nih.gov/projects/GeneRIF/ and ftp://ftp.ncbi.nih.gov/gene/GeneRIF/) GSEA : Gene Set Enrichment Analysis; categories compiled by the Broad Institute (website: http://www.broad.mit.edu/gsea/index.jsp, reference: Subramanian et al. (2005) ; Mootha, et al. (2003)) KEGG : Kyoto Encyclopedia of Genes and Genomes (KEGG) derived from the KEGG.db package. MP : Mouse phenotype (reference: Bult et al. (2008); website: http://www.informatics.jax.org/) CTD : Comparative Toxicogenomics Database transfac : Transfac derived categories.

Details

Package:	CLEAN.Mm
Type:	Package
Version:	1.0.0
Date:	2009-03-30
License:	GPL>=2
LazyLoad:	yes

Use CLEAN.Mm() to display available category types.

Author(s)

Johannes Freudenberg, Mario Medvedovic

Maintainer: Mario Medvedovic <[e-mail]>

References

Subramanian, Tamayo, et al. (2005, PNAS 102, 15545-15550) Mootha, Lindgren, et al. (2003, Nat Genet 34, 267-273) Bult CJ, Eppig JT, Kadin JA, Richardson JE, Blake JA; and the members of the Mouse Genome Database Group. 2008. The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res 36(Database issue):D724-8.

See Also

CLEAN

Examples

library(CLEAN)
CLEAN.Mm()
functionalCategories <- getFunctionalCategories(CLEAN.Mm(), species = "Mm")
### not run
#library(CLEAN)
#data(gimmOut)
#runCEAN(gimmOut, functionalCategories = getFunctionalCategories(CLEAN.Mm(), species = "Mm")) 

uc-bd2k/CLEAN.Mm documentation built on Oct. 23, 2022, 6:10 a.m.