MS_getPathIds: Get pathway identifiers of a given organism

In MetaboSignal: MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways

Description

This function retrieves the identifiers (IDs) of all metabolic and signaling KEGG pathways of a given organism. These pathway IDs can be used to build a MetaboSignal network with the function "MS_keggNetwork( )".

Usage

MS_getPathIds(organism_code)

Arguments

organism_code

character vector containing the KEGG code for the organism of interest. For example the KEGG code for the rat is "rno". See the function "MS_keggFinder( )".

Value

This function returns a matrix, where each row contains the ID, description, category, and type (i.e. "metabolic" or "signaling") of each pathway. This matrix is also exported in a file named "organism-code_pathways.txt".

References

Tenenbaum, D. KEGGREST: Client-side REST access to KEGG. R package version >= 1.17.0.

Examples

rat_paths <- MS_getPathIds(organism_code = "rno")
human_paths <- MS_getPathIds(organism_code = "hsa")

MetaboSignal documentation built on Nov. 8, 2020, 6 p.m.