downloadPathways {EnrichmentBrowser} | R Documentation

## Download of KEGG pathways for a particular organism

### 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 <Ludwig.Geistlinger@sph.cuny.edu>

### See Also

`keggList`, `keggGet`, `KEGGPathway`, `parseKGML`

### Examples

            pwys <- downloadPathways("hsa")

[Package EnrichmentBrowser version 2.22.2 Index]