KeggEnzymeConn {biodbKegg} | R Documentation |
The connector class to KEGG Enzyme database.
The connector class to KEGG Enzyme database.
This is a concrete connector class. It must never be instantiated directly,
but instead be instantiated through the factory BiodbFactory
.
Only specific methods are described here. See super classes for the
description of inherited methods.
biodb::BiodbConnBase
-> biodb::BiodbConn
-> biodbKegg::KeggConn
-> KeggEnzymeConn
new()
New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.
KeggEnzymeConn$new(...)
...
All parameters are passed to the super class initializer.
Nothing.
getPathwayIds()
Gets organism pathways. This method retrieves KEGG pathways of the specified organism in which the enzymes are involved.
KeggEnzymeConn$getPathwayIds(id, org)
id
A character vector of KEGG Compound IDs.
org
The organism in which to search for pathways, as a KEGG organism code (3-4 letters code, like 'hsa', 'mmu', ...). See https //www.genome.jp/kegg/catalog/org_list.html for a complete list of KEGG organism codes.
A vector of KEGG pathway IDs.
clone()
The objects of this class are cloneable with this method.
KeggEnzymeConn$clone(deep = FALSE)
deep
Whether to make a deep clone.
# Create an instance with default settings: mybiodb <- biodb::newInst() # Get connector conn <- mybiodb$getFactory()$createConn('kegg.enzyme') # Get pathway IDs related to enzymes pathway.ids=conn$getPathwayIds(c('1.2.1.3', '3.7.1.3'), org='mmu') # Terminate instance. mybiodb$terminate()