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

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

Description

This function generates the gene set of a pathway.

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.

Author(s)

Frank Kramer

Examples

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

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