pathview with tomato and minor species
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Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 10 weeks ago
United States
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?
Pathways pathview Pathways pathview • 1.0k views
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