rBiopaxParser (version 2.10.0)

listPathwayComponents: This function lists all pathway components of a given pathway.

Description

This function returns a (unique) data.frame listing all component IDs, names and classes of the supplied pathway.

Usage

listPathwayComponents(biopax, id, includeSubPathways = TRUE, returnIDonly = FALSE, biopaxlevel = 3)

Arguments

biopax

A biopax model

id

string. A pathway ID

includeSubPathways

logical. If TRUE the returned list will include subpathways and pathwaysteps as well.

returnIDonly

logical. If TRUE only IDs of the components are returned. This saves tiem for looking up names for every single ID.

biopaxlevel

integer. Set the biopax level here if you supply a data.table directly.

Value

data.frame

Examples

# load data
 data(biopaxexample)
 listPathwayComponents(biopax, id="pid_p_100002_wntpathway")