getGenome: Retrieve a genome from the OMA Browser database

In OmaDB: R wrapper for the OMA REST API

Description

This function obtains the basic information for one specific genome available on the OMA Browser, or - if no id is provided - a dataframe with all available genomes.

Usage

getGenome(id = NULL, attribute = NULL)

Arguments

id	A genome identifier. By default, all available genomes will be returned.
attribute	An extra attribute to be returned (proteins)

Details

Ids can be either the scientific name of a species, the NCBI taxonomy id or the UniProtKB mnemonic species code.

The optional argument attribute can be used to directly load the proteins belonging to the genome. Alternatively, you can access the proteins attribute of the result which will transparently load the proteins from the OMA Browser.

Value

an object containing the JSON keys as attributes or a dataframe

Examples

getGenome()
getGenome(id='HUMAN')
getGenome(id=9606)
getGenome(id='HUMAN',attribute='proteins')

OmaDB documentation built on Nov. 13, 2020, 2 a.m.