R wrapper for the OMA REST API

Documentation for package ‘OmaDB’ version 2.6.1

Help Pages

OmaDB-package	OmaDB: A package for the orthology prediction data download from OMA database.
$.omadb_obj	Resolve URLs automatically when accessed
annotateSequence	Map GO annotation to a sequence that is not available in the OMA Browser
formatTopGO	Format the GO annotations data
getAttribute	Get the value for the Object Attribute
getGenome	Retrieve a genome from the OMA Browser database
getGenomePairs	Retrieves the pairwise relations among two genomes
getHOG	Retrieve a HOG from the OMA Browser
getLocus	Get loci for a given list of proteins
getObjectAttributes	Get the Object Attributes
getOMAGroup	Retrieve an OMA Group from the OMA Browser
getProtein	Retrieve a protein from the OMA Browser
getTaxonomy	Get the Taxonomic tree function
getTopGO	Get the topGO Object function
getTree	Get the Tree Object
getVersion	Get the API and database version function
group	An example OMA group object.
hog	An example HOG object.
mapSequence	Map the Protein Sequence Function
OmaDB	OmaDB: A package for the orthology prediction data download from OMA database.
orthologs	An example orthologs object.
pairs	An example genome alignment object.
protein	An example protein object.
resolveURL	Load data for a given url from the OMA Browser API.
searchProtein	Get the CrossReferences in the OMA database for a pattern
sequence_annotation	An example dataframe containing GO annotations identified from a given sequence.
sequence_map	An example dataframe containing proteins identified from a given sequence.
setAPI	Set the url to the OMA Browser API
taxonomy	An example newick format taxonomy object.
xref	An example xref object.