MS_changeNames: Transform KEGG IDs into common names

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

Description

This function allows transforming KEGG IDs of genes or compounds into their corresponding common names (for compounds) or symbols (for genes).

Usage

MS_changeNames(nodes, organism_code)

Arguments

nodes	character vector or matrix containing the KEEG IDs of either metabolites, genes (organism-specific or orthology), or reactions. It also converts human Entrez gene IDs into symbols.
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( )". This argument is ignored when nodes are metabolites.

Value

A character string or a matrix containing the common metabolite names or gene symbols corresponding to the input KEGG IDs. Reaction IDs remain unchanged.

References

http://www.kegg.jp/kegg/docs/keggapi.html

Examples

MS_changeNames(c("rno:84482", "K01084", "cpd:C00267"), "rno")
MS_changeNames("K01082", organism_code = "rno")

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