brendaDb: The BRENDA Enzyme Database

ID2Enzyme

R Documentation

A helper function for converting names/synonyms to EC numbers.

Description

A helper function for converting names/synonyms to EC numbers.

Usage

ID2Enzyme(brenda, ids)

Arguments

`brenda`	A `tibble` generated from `ReadBrenda()`.
`ids`	A character vector of IDs to be converted.

Details

The function goes through "RECOMMENDED_NAME", "SYSTEMATIC_NAME", and "SYNONYMS" in the BRENDA file, and uses regexes to look for the given IDs. Values in the three columns are kept if the regex had a hit, otherwise NA is filled. The function can take in IDs of multiple sources, e.g. c("ADH4", "CD38", "pyruvate dehydrogenase"). Note that using aliases instead of symbols could lead to false positives in the output table.

Value

A tibble with columns ID, EC, and at least one of (RECOMMENDED_NAME, SYSTEMATIC_NAME and SYNONYMS).

Examples

df <- ReadBrenda(system.file("extdata", "brenda_download_test.txt",
                          package = "brendaDb"))
ID2Enzyme(df, c("CD38", "ADH4", "pyruvate dehydrogenase"))

y1zhou/brendaDb documentation built on Dec. 12, 2022, 3:43 a.m.