getProtein: Retrieve a protein from the OMA Browser

In klarakaleb/roma: R wrapper for the OMA REST API

Retrieve a protein from the OMA Browser

Description

This function enables to retrieve information on one or several proteins from the OMA Browser database.

Usage

getProtein(id, attribute = NULL)

Arguments

id	Identifier(s) for the entry or entries to be returned. a character string if single entry or a vector if multiple.
attribute	Instead of the protein, return the attribute property of the protein. Attriute needs to be one of 'domains', 'orthologs', 'gene_ontology', 'locus', or 'homoeologs'.

Details

In its simplest form the function returns the base data of the query protein. The query protein can be selected with any unique id, for example with a UniProtKB accession (P12345), an OMA id (YEAST00012), or a RefSeq id (NP_001226). To retrieve more than one protein, you should pass a vector of IDs.

Non-scalar properties of proteins such as their domains, GO annotations, orthologs or homeologs will get loaded upon accessing them, or if you only need this information you can set the attribute parameter to the property name and retrieve this information directly.

Value

An object containing the JSON keys as attributes or a dataframe containing the non-scalar protein property.

See Also

For non-unique non-unique IDs or partial ID lookup, use searchProtein instead.

Examples

getProtein(id='YEAST00001')
getProtein(id='YEAST00001', attribute='orthologs')
getProtein(id=c('YEAST00001','YEAST00002','YEAST00012'))
getProtein(id=c('YEAST00001','YEAST00002','YEAST00012'), attribute='gene_ontology')

klarakaleb/roma documentation built on April 21, 2024, 8:39 a.m.