Built-in RData


As part of the package, the built-in RData (with .RData extension; available at RData) contain curated/compiled data, which can be broadly grouped into the following categories:

  • Ontologies

Ontologies include Gene Ontology (GO) and its three subontologies (BP: Biological Process; MF: Molecular Function; CC: Cellular Component), Human Phenotype (HP) and its four subontologies (PA: Phenotypic Abnormality; CM: Clinical Modifier; MI: Mode of Inheritance; MA: Mortality Aging), Disease Ontology (DO), and Mammalian Phenotype (MP). Terms in an ontology are organised as a direct acyclic graph (DAG), which is further stored as an object of the class igraph.

  • Organism-specific databases

Organisms supported are: human (Hs; tax_id=10090), mouse (Mm; tax_id=10090), arabidopsis (At; tax_id=3702), c.elegans (Ce; tax_id=6239), fruitfly (Dm; tax_id=7227), zebrafish (Da; tax_id=7955), rat (Rn; tax_id=10116) and chicken (Gg; tax_id=9031). For example, human-specific databases contain information on Entrez Genes, their annotations by a variety of ontologies, their evolutionary age (or called 'phylostratific age', PS), their assigned domain superfamilies (SF), and their interacting network derived from STRING.

  • Genesets in human

These genesets are derived from the molecular signatures database (Msigdb).

  • Datasets as demos

They are used in Demos.


For details, please refer to Documentations.