Limit Findsimilar() To A Subset Of Genes In The Whole Cufflinks Data Set [Cummerbund]

Question

[wadunn83]

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. R is a necessary tool that I use, but I am not fluent. Basically, at the conversational level, probably. So maybe (I hope) I am missing something.

A quick description of what I would like to do:

• 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