[BioC] pathview with tomato and minor species

[Luo Weijun]

Hi Peter,
Sorry for the late response. I noticed that Solanum lycopersicum (tomato) has been added to KEGG recently. To solve your problem, I updated korg data and included over 600 more recently added species, including tomato. So pathview now works with 3000 species with the latest KEGG additions.

You should be able to download/install the new pathview release from:
http://bioconductor.org/packages/release/bioc/html/pathview.html

If you want to do gene set/pathway analysis for you tomato data, gage (and pathview) devel version has also been updated correspondingly:
http://bioconductor.org/packages/2.14/bioc/html/gage.html
http://bioconductor.org/packages/2.14/bioc/html/pathview.html
HTH
Weijun

--------------------------------------------
On Thu, 2/20/14, Peter wrote:

 Good morning/afternnoon
 Luo,
 I am a relatively new user to R bioconductor and
 have been learning the Pathview package you wrote to present
 tomato expression data on a KEGG pathway.

 I have however run into a issue with the
 data(korg) part of the 'pathview package'. There is
 no listing for tomato in this package however when I looked
 at the 'download.kegg' function I noticed that this
 function links to a 'KEGG database' (http://www.genome.jp/...)
 to get the xml and png files. Upon further investigation I
 have found that this 'KEGG database' does have xml
 and png files for all the Solanum lycopersicum (tomato)
 pathways.


 In my relatively basic way I tried adding a line
 for tomato to the 'korg object' using the below
 script








 data(korg)korg
 <-rbind(korg,c("sly",
 "Solanum
 lycopersicum",
 "tomato",
 "1","101267560","101267560"))
 .. however this did not work =(
 I was wondering if you could give me a snippet to
 fix this problem ? or point me in the write
 direction

 Thank you for taking the time to read this
 email

 Kind regards,
 Peter