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cufflinks cummeRbund set condition Jetse Bioinformatics 1 12-11-2012 04:48 AM

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Old 09-06-2013, 08:31 PM   #1
Location: Irvine CA, USA

Join Date: Dec 2009
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Default Limit findSimilar() to a subset of genes in the whole Cufflinks data set [cummeRbund]

Hello folks,

I am running into what I hope is not a fundamental limitation of cummeRbund's `findSimilar()` function.

findSimilar is supposedly an object method of class CuffSet (itself being basically an interface to the SQLite DB tables). So I can't really figure out a straightforward way to run findSimilar() on a set of genes that is LESS than the entire cufflinks experiment. However, I am a Python guy, so maybe (I hope) I am missing something.

A quick example of what I would like to do is:
  • I have a list of genes that are 1-to-1 orthologs in multiple species
  • One of these genes has an RNA abundance profile that I am keen on
  • I would like to pull out the top 'n' genes with similar abundance profiles THAT ARE ALSO 1-to-1 ORTHOLOGS like geneX
  • I have a list of these 1-to-1 ortholog genes and a CuffGeneSet object initialized with them

Can anyone help me figure this out?


In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.
--Stephen Jay Gould
Gus is offline   Reply With Quote
Old 03-23-2014, 11:24 AM   #2
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Location: UK

Join Date: Mar 2014
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I can help you do this if you're still interested. Need more details.
urostor is offline   Reply With Quote

cummerbund, findsimilar

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