rBiopaxParser (version 2.10.0)

pathway2Geneset: This function generates the gene set of a pathway.

Description

This function generates a gene set of all physicalEntity's of a pathway. First all interactions of the pathway are retrieved and all components of these interactions are then listed.

Usage

pathway2Geneset(biopax, pwid, returnIDonly = FALSE, biopaxlevel = 3)

Arguments

biopax

A biopax model

pwid

string

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

Returns the gene set of the supplied pathway. Returns NULL if the pathway has no components.

Examples

# load data
 data(biopaxexample)
 pwid1 = "pid_p_100002_wntpathway"
 pathway2Geneset(biopax, pwid=pwid1)