rBiopaxParser (version 2.10.0)

downloadBiopaxData: This function downloads Biopax data from online databases

Description

This function has an internal list of download links for some online databases. It will retrieve the selected model from the selected database using RCurl. The downloaded file is (if needed) unzipped and ready to be used as input for rBiopaxParser::readBiopax. This function requires package RCurl to run. You can easily skip this step by downloading the exported file yourself and continuing with readBiopax.

Usage

downloadBiopaxData(database = "NCI", model = c("pid", "biocarta", "reactome", "kegg"), outputfile = "", version = "biopax2")

Arguments

database

string. Select which database you want to download from. Currently only NCI links have been stored.

model

string. Select which model/file you want to download. Currently NCI versions of the Pathway Interaction Database, Biocarta, Reactome and KEGG are linked.

version

string. Select which Biopax Version you want to download.

outputfile

string. The file name to save the downloaded data in. If left empty the URL file name will be used. The unzipped file name can be different from this. Check the screen output of gunzip.

Value

none. Check output for the name of the unzipped biopax .owl file.

Examples

## Not run: file = downloadBiopaxData("NCI", "biocarta", version = "biopax2")
 ## Not run: biopax = readBiopax(file)
 ## Not run: biopax