inst/staticdocs/RData_tmp.md

In hfang-bristol/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 http://dnet.r-forge.r-project.org/data) contain curated/compiled data, which can be broadly grouped into the following categories:

• Ontologies

Locate in the subdirectory Obo, containing information on ontology terms and their relationships. Ontologies include Gene Ontology (GO) and its three subontologies (BP: Biological Process; MF: Molecular Function; CC: Cellular Component), Human Phenotype (HP) and its three subontologies (PA: Phenotypic Abnormality; ON: ONset and clinical course; MI: Mode of Inheritance), 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

Locate in the subdirectory Msigdb. These genesets are derived from the molecular signatures database.

• Datasets as demos

Locate in the subdirectory Datasets. They are used in Demos

Documentations and Download

For details, please refer to Documentations.

In addition to download (as shown above), the Linux/Mac user can use shell commands in Terminal for download in one go:

# recursively download all RData files (preserving the whole directory structure)
wget -r -l2 -A "*.RData" -np -nH --cut-dirs=0 "http://dnet.r-forge.r-project.org/data" 
# view the download
ls -lh -R data

hfang-bristol/dnet documentation built on Feb. 23, 2020, 2:06 p.m.