downloadPathways: Download of KEGG pathways for a particular organism

Description Usage Arguments Value Author(s) See Also Examples

View source: R/downloadKEGGPathways.R

Description

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

Usage

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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 <Ludwig.Geistlinger@sph.cuny.edu>

See Also

keggList, keggGet, KEGGPathway, parseKGML

Examples

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        pwys <- downloadPathways("hsa")
    

lgeistlinger/EnrichmentBrowser documentation built on July 26, 2021, 9:54 p.m.