getProtein: Retrieve a protein from the OMA Browser

Description Usage Arguments Details Value See Also Examples

View source: R/getProtein.R

Description

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

Usage

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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

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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 Nov. 11, 2020, 5:36 a.m.