getKGMLurl {KEGGgraph} | R Documentation

## Get KGML file (url) with KEGG PATHWAY ID and (optional) organism

### Description

The function simply returns the KGML file url given KEGG PATHWAY ID. If the KEGG PATHWAY ID contains no organism prefix, user can specify the 'organism' parameter. Otherwise the 'organism' option is ignored.

retrieveKGML is a simple wrapper to getKGMLurl, which downloads the KGML file with `download.file` in utils package.

### Usage

    getKGMLurl(pathwayid, organism = "hsa")
    retrieveKGML(pathwayid, organism, destfile,method="wget", ...)

### Arguments

`pathwayid` | KEGG PATHWAY ID, e.g. 'hsa00020'
`organism` | three-alphabet organism code, if pathwayid contains the ocde this option is ignored
`destfile` | Destination file, to which the remote KGML file should be saved
`method` | Method to be used for downloading files, passed to `download.file` function. Currently supports "internal", "wget" and "lynx"
`...` | Parameters passed to download.file

### Details

The function `getKGMLurl` takes the pathway identifier (can be in the form of 'hsa00020' or with 'pathway' prefix, for example 'path:hsa00020'), and returns the url to download KGML file.

The mapping between pathway identifier and pathway name can be found by KEGGPATHNAME2ID (or reversed mappings) in KEGG.db package. See vignette for example.

`retrieveKGML` calls `download.file` to download the KGML file from KEGG FTP remotely.

### Value

KGML File URL of the given pathway.

### Note

So far the function does not check the correctness of the 'organism' prefix, it is the responsibility of the user to garantee the right spelling.

### Author(s)

Jitao David Zhang mailto:j.zhang@dkfz.de

### Examples

    getKGMLurl("hsa00020")
    getKGMLurl("path:hsa00020")
    getKGMLurl("00020",organism="hsa")

    ## NOT RUN
    tmp <- tempfile()
    retrieveKGML(pathwayid='00010', organism='cel', destfile=tmp, method="wget")

[Package KEGGgraph version 1.1.0 Index]