pathway2Geneset {rBiopaxParser} | R Documentation |
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.
pathway2Geneset(biopax, pwid, returnIDonly = FALSE, biopaxlevel = 3)
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. |
Returns the gene set of the supplied pathway. Returns NULL if the pathway has no components.
Frank Kramer
# load data data(biopaxexample) pwid1 = "pid_p_100002_wntpathway" pathway2Geneset(biopax, pwid=pwid1)