integrateNetwork: 'integrateNetwork' generate an integrated network

In kwanjeeraw/grinnWeb: Graph database and R package for omics integration

Description

from the list of metabolites, find and connect these metabolites through four type of relationships including biochemical reaction, enzyme catalysis, encoding gene and metabolic pathway.

Usage

integrateNetwork(txtInput, organism, returnAs="json", searchBy="grinn")

Arguments

txtInput	string containing metabolite ids. Metabolite ids are from the specified database, see searchBy. Default is grinn id e.g. C00065. Search using grinn ids, txtInput is in the following format: txtInput = "['id'1, 'id2']". Search using other database ids, txtInput must be in the following format: txtInput = "['databaseName:id'1, 'databaseName:id2']".
organism	string of species in the following format: organism = "'species'"
returnAs	string of output type. Specify the type of the returned network. It can be "all", "json" or "cytoscape", but default is "json". "cytoscape" is the format used in Cytoscape.js
searchBy	string of database name. Specify the database of which the ids used as the txtInput, see txtInput. It can be "grinn" or "InChI" or "KEGG" or "PubChem" or "ChEBI". Default is "grinn".

Value

list of nodes and edges encapsulated in json format. Return empty list if found nothing.

Author(s)

Kwanjeera W [e-mail]

References

Modify the output generation for Cytoscape.js from https://github.com/cytoscape/r-cytoscape.js/blob/master/cytoscapeJsSimpleNetwork.R

Cytoscape.js, Network library for analysis and visualisation http://js.cytoscape.org/

See Also

http://js.cytoscape.org/

Examples

# Query metabolites by PubChem ids and build a network
txtInput <- "['PubChem:3326','PubChem:3436','PubChem:7656']"
organism <- "'Homo sapiens'"
result <- integrateNetwork(txtInput, organism, returnAs="all", searchBy="PubChem")
# Query metabolites by grinn ids and build a network
txtInput <- "['C00024','C00136','C05269']"
organism <- "'Homo sapiens'"
result <- integrateNetwork(txtInput, organism, returnAs="all", searchBy="grinn")

kwanjeeraw/grinnWeb documentation built on May 20, 2019, 7:07 p.m.