downloadBiopaxData: This function downloads Biopax data from online databases

In rBiopaxParser: Parses BioPax files and represents them in R

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.
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.
version	string. Select which Biopax Version you want to download.

Value

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

Author(s)

fkramer

Examples

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

Example output

Loading required package: data.table

rBiopaxParser documentation built on Nov. 8, 2020, 8:21 p.m.