Question: Use of makeSPIAdata function from SPIA on non human organisms
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gravatar for Fabio Marroni
2.4 years ago by
Fabio Marroni2.1k
Italy
Fabio Marroni2.1k wrote:

I am trying to use the Bioconductor package SPIA to analyze KEGG pathways in Vitis vinifera. The first step is to import the KEGG xml file into the SPIA format using makeSPIAdata and this should generate an .Rdata object for downstream analysis.

I tried downloading a random pathway in Vitis by pressing "Download KGML" on this link and saving in the test directory, but when running the command

makeSPIAdata(kgml.path="test/",organism="vvi",out.path="SPIA_pathways/")

The function returned the value

[[1]] FALSE

And no file was saved.

Trying the same using a random human pathway, as this one gave no problem.

The function returned

[[1]] TRUE

And the file was created.

Can someone help with this issue?

EDIT: December 6, 2016 Further trials showed that not all the pathways give error (but several of them do!) and I was unlucky in selecting several pathways that all gave error. I can provide updates on my trials if someone is interested, otherwise I will not provide further updates.

kegg bioconductor R • 792 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Fabio Marroni2.1k
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