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Last data update: 2014.03.03

R: download_KEGGfile

download_KEGGfile

R Documentation

download_KEGGfile

Description

The function download XML files and png files from KEGG website to local disk

Usage

download_KEGGfile(pathway_id = "00010", species = "hsa",
  target_dir = getwd())

Arguments

`pathway_id`	the KEGG pathway id, such as '00010'
`species`	the species id in KEGG database, 'hsa' means human, 'mmu' means mouse, 'rno' means rat, etc
`target_dir`	the local directory where the downloaded files are saved

Details

If pathway_id is set as 'all', all KEGG pathway ids in KEGG.db package will be used and downloaded from KEGG website

Examples

download_KEGGfile(pathway_id="00010",species='hsa')

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(KEGGprofile)

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/KEGGprofile/download_KEGGfile.Rd_%03d_medium.png", width=480, height=480)
> ### Name: download_KEGGfile
> ### Title: download_KEGGfile
> ### Aliases: download_KEGGfile
> 
> ### ** Examples
> 
> download_KEGGfile(pathway_id="00010",species='hsa')
[1] "Downloading files: 1/1"
trying URL 'http://www.genome.jp/kegg-bin/download?entry=hsa00010&format=kgml'
Content type 'text/xml' length unknown
.......... .......... .......... .......... .....
downloaded 45 KB

trying URL 'http://www.genome.jp/kegg/pathway/hsa/hsa00010.png'
Content type 'image/png' length 28060 bytes (27 KB)
==================================================
downloaded 27 KB

trying URL 'http://www.genome.jp/kegg/pathway/map/map00010.png'
Content type 'image/png' length 26645 bytes (26 KB)
==================================================
downloaded 26 KB

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> dev.off()
null device 
          1 
>