Description

An R object that contains associations between HPCM terms and Mouse Entrez Genes. This data is first prepared based on http://purl.obolibrary.org/obo/hp.obo and http://compbio.charite.de/hudson/job/hpo.annotations.monthly/lastStableBuild/artifact/annotation/ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype.txt, which results in annotations of Human Entrez Genes. Then, these annotations are transferred to Mouse Entrez Genes based on ftp://anonymous@ftp.ncbi.nih.gov/pub/HomoloGene/build67/homologene.data.

Usage

org.Mm.egHPCM <- dRDataLoader(RData = "org.Mm.egHPCM")

Value

an object of class "GS", a list with following components:

• set_info: a matrix of nSet X 4 containing gene set information, where nSet is the number of gene sets (i.e. HPCM terms), and the 4 columns are "setID" (i.e. "Term ID"), "name" (i.e. "Term Name"), "namespace" and "distance"
• gs: a list of gene sets, each storing gene members thereof. Always, gene sets are identified by "setID" and gene members identified by "Entrez ID"

References

Robinson et al. (2012) The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am J Hum Genet, 83:610-615.

Sayers et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res, 39:D38-51.

Examples

org.Mm.egHPCM <- dRDataLoader(RData='org.Mm.egHPCM')

'org.Mm.egHPCM' (from https://github.com/hfang-bristol/RDataCentre/blob/master/dnet/1.0.7/org.Mm.egHPCM.RData?raw=true) has been loaded into the working environment (at 2018-01-19 12:38:40)
names(org.Mm.egHPCM)

[1] "gs"       "set_info"