inst/staticdocs/RData.md

In dnet: Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

Introduction

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.

Documentations

For details, please refer to Documentations.

dnet documentation built on Feb. 20, 2020, 5:08 p.m.