Bioconductor Digest, Vol 93, Issue 26: How to create KEGG's pathway data for SPIA?
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Tarca, Adi ▴ 570
@tarca-adi-1500
Last seen 21 months ago
United States
>Dear all, >I want to use SPIA to analyze expression data for rice (oriza sativa - >osa). There is KEGG's pathway data for rice, but rice is not among those >organism in the extData directory of the SPIA package. Does anyone has >created their own pathway data to give it as input to the function spia? If >so, what are the steps one has to follow to get the pathway data in the list >format of path.info? As reference, path.info for human can be loaded into R >like this: load(file = paste(system.file("extdata/hsaSPIA.RData", package = >"SPIA"))) >Thank you! >Lourdes Hi Lourdes, The KEGG data on which SPIA runs is provided in the SPIA's /extdata folder only for a few (most popular) organisms. The package size was the reason why I do not provide these data for all KEGG organisms. For the osa organism that you asked about, I made the data available at: http://bioinformaticsprb.med.wayne.edu/SPIA/build09222010/ I plan to make it available for all organisms in KEGG soon. The parser from KEGG xml files into SPIA's path.info objects for any organism is not packaged at this point. If you need to parse the xml files yourself you can take a look the KEGGgraph package that can provide some help yet it won't be straightforward mainly because a node in a KEGG signaling pathway is not always made of a single gene. I hope this helps. Adi Tarca
Organism KEGGgraph SPIA Organism KEGGgraph SPIA • 961 views
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