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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
Gus
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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?

Thanks,

Gus
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Old 03-23-2014, 11:24 AM   #2
urostor
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Bump.
I can help you do this if you're still interested. Need more details.
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