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 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.
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.