find_chebis: Find ChEBI IDs for name patterns

In protti: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

Find ChEBI IDs for name patterns

Description

Search for chebi IDs that match a specific name pattern. A list of corresponding ChEBI IDs is returned.

Usage

find_chebis(chebi_data, pattern)

Arguments

chebi_data

a data frame that contains at least information on ChEBI IDs (id) and their names (name). This data frame can be obtained by calling fetch_chebi(). Ideally this should be subsetted to only contain molecules of a specific type e.g. metals. This can be achieved by calling find_all_subs with a general ID such as "25213" (Metal cation) and then subset the complete ChEBI database to only include the returned sub-IDs. Using a subsetted database ensures better search results. This is a helper function for other functions.

pattern

a character vector that contains names or name patterns of molecules. Name patterns can be for example obtained with the split_metal_name function.

Value

A list of character vectors containing ChEBI IDs that have a name matching the supplied pattern. It contains one element per pattern.

protti documentation built on Oct. 22, 2024, 1:06 a.m.