BiocycPathwayEnzymes: Get all EC numbers involved in a BioCyc pathway.

Description Usage Arguments Value Examples

View source: R/biocyc.R

Description

Get all EC numbers involved in a BioCyc pathway.

Usage

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BiocycPathwayEnzymes(org.id = "HUMAN", pathway, sleep = 0)

Arguments

org.id

The identifier for the organism database in BioCyc, e.g. ECOLI, HUMAN, META, AFER243159

pathway

A case-sensitive pathway object identifier, e.g. PWY66-400, LYSINE-DEG1-PWY.

sleep

Optional, default is 0. If set to a non-zero value, pause for the specified seconds after retrieving each reaction. Increase this if the default fails (probably limited on the BioCyc API side).

Value

If the pathway is found, returns a tibble with columns - RxnID: reaction IDs found in the pathway. - EC: EC number of the enzyme catalyzing the reaction. - ReactionDirection: direction of the reaction. - LHS: left-hand-side of the reaction. - RHS: right-hand-side of the reaction. Different compounds in the reactions are separated by " + " in columns LHS and RHS. The function returns NULL if the pathway ID is not found.

Examples

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BiocycPathwayEnzymes("HUMAN", "PWY66-400")

y1zhou/brendaDb documentation built on July 24, 2021, 7:14 p.m.