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

In frankkramer-lab/rBiopaxParser: Parses BioPax files and represents them in R

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

Author(s)

Frank Kramer

Examples

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

frankkramer-lab/rBiopaxParser documentation built on July 19, 2020, 9:49 a.m.