Limit findSimilar() to a subset of genes in the whole Cufflinks data set [cummeRbund]

[Gus]

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

[urostor]

Bump.
I can help you do this if you're still interested. Need more details.