downloadPathways: Download of KEGG pathways for a particular organism

In EnrichmentBrowser: Seamless navigation through combined results of set-based and network-based enrichment analysis

Description

The function downloads all metabolic and non-metabolic pathways in KEGG XML format for a specified organism.

Usage

downloadPathways(org, cache = TRUE, out.dir = NULL, zip = FALSE)

Arguments

org	Organism in KEGG three letter code, e.g. ‘hsa’ for ‘homo sapiens’.
cache	Logical. Should a locally cached version used if available? Defaults to TRUE.
out.dir	Output directory. If not null, pathways are written to files in the specified directory.
zip	Logical. In case pathways are written to file (‘out.dir’ is not null): should output files be zipped?

Value

if(is.null(out.dir)): a list of KEGGPathway objects else: none, as pathways are written to file

Author(s)

Ludwig Geistlinger <[e-mail]>

See Also

keggList, keggGet, KEGGPathway, parseKGML

Examples

    
        pwys <- downloadPathways("hsa")
    

EnrichmentBrowser documentation built on Dec. 12, 2020, 2 a.m.