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

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

Description

Provide functional specific to Rattus norvegicus to the CLEAN package. GO : Gene Ontolgy categories derived from packages GO.db and org.Rn.eg.db chrLoc: Cytogenetic bands, derived from the org.Rn.eg.db package CpGislands: CpG islands within 4kb upstream and 1kb downstream of the TSS based on data from UCSC genome browser (website: http://genome.ucsc.edu/) ESR1targets: Experimentally derived Estrogen Receptor alpha targets. (Reference: Carroll et al. (2006)) 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. methylome : Experimentally derived hyper-methylation and hypo-methylation loci related to breast cancer, references: (Cheng et al. (2008), Novak et al. (2008)) 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.Rn
Type:	Package
Version:	1.0.0
Date:	2011-01-14
License:	GPL>=2
LazyLoad:	yes

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

uc-bd2k/CLEAN.Rn documentation built on March 5, 2020, 5:24 p.m.