MS_keggFinder: Get KEGG IDs for compounds, organisms or pathways

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

Description

This function returns a list of entries corresponding to one of the following KEGG databases: "compound", "organism", "pathway". It can also find entries with matching query keywords in a given database.

Usage

MS_keggFinder(KEGG_database, match = NULL, organism_code)

Arguments

KEGG_database	character vector containing the name of the KEGG database of interest: "compound", "organism", "pathway".
match	character vector containing one or more elements (i.e. key words) to be matched as compound names.
organism_code	character vector containing the KEGG code for the organism of interest. For example the KEGG code for the rat is "rno". This argument is only required for KEGG_database = "pathway".

Value

By default, a matrix where each row contains the KEGG entries of the database of interest. When using the option "match" a list is returned, each list element containing information of matched entries.

Examples

MS_keggFinder(KEGG_database = "compound", match = "acetoacetic acid")

MS_keggFinder(KEGG_database = "organism", match = c("rattus","human"))

MS_keggFinder(KEGG_database = "pathway", match = c("glycol", "insulin signal", "akt"),
            organism_code = "rno")

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