getKGMLurl {KEGGgraph} | R Documentation |
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.
getKGMLurl(pathwayid, organism = "hsa") retrieveKGML(pathwayid, organism, destfile,method="wget", ...)
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 |
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.
KGML File URL of the given pathway.
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.
Jitao David Zhang mailto:j.zhang@dkfz.de
getKGMLurl("hsa00020") getKGMLurl("path:hsa00020") getKGMLurl("00020",organism="hsa") ## NOT RUN tmp <- tempfile() retrieveKGML(pathwayid='00010', organism='cel', destfile=tmp, method="wget")