retrieveKGML.new: Retrieve the KGML file of a KEGG pathway

In uc-bd2k/paslincs: Pathway activity signatures from LINCS L1000 consensus gene signatures

Description

Retrieve the KGML file of a KEGG pathway

Usage

retrieveKGML.new(pathway, organism, destfile, method = "auto", ...)

Arguments

pathway	A character value of KEGG pathway ID as in EdgeInfo.
organism	A character value of the three- or four-letter KEGG organism code (see organism code at: https://www.genome.jp/kegg-bin/get_htext?br08601.keg).
destfile	The output file, to which the KGML file is saved.
method	A character value of the method used to download file. Default is "auto". See details of KEGGgraph::retrieveKGML (https://www.rdocumentation.org/packages/KEGGgraph/versions/1.30.0/topics/getKGMLurl).

Value

The KGML file is saved in the specified file destfile.

Examples

tmp<- tempfile()
retrieveKGML.new("hsa04150","hsa",tmp)

uc-bd2k/paslincs documentation built on May 28, 2020, 8:20 a.m.