getReactomeBiopax: Download biopax files for reactome pathways.

In biodev/packageDir: Tool for in silico functional analysis design and exploration of relation between genomic function and aberration.

Description

Attempts to download biopax files for reactome pathways. First, pathway's individual database identifiers are obtained from bioMART, then restful calls are made to Reactome's restful interface. A record of successfully downloaded pathways is made in the file "./reference_data/paths/biopax/record_of_biopax_pathways.txt" so that pathways will not be repeatedly downloaded.

Usage

getReactomeBiopax(study, pathNames, verbose = T)

Arguments

study	A Study object.
pathNames	The names of the pathways the program should attempt to download.
verbose	logical flag indicating if user should be prompted before attempted download of biopax pathways.

Value

Character vector containing the names of any pathways that could not be downloaded.

biodev/packageDir documentation built on Nov. 4, 2019, 7:19 a.m.