[BioC] Motif enrichment analysis: Error in transfac format and background frequencies from BSGenome

[deepti anand]

Hi Roberts,
Thank you for suggestion. The backgrounds available in PWMEnrich for mouse are in mm9 assembly (current is mm10). Also, I found that it has 329 PWMs which is less than current MotifDb (528 motifs). That is why I want to create a background with the current mouse genome and use 528 motifs for enrichment analysis in my gene list  Could you please tell me how can I export the motifs in 'transfac ' format and get the background frequencies from 'BSgenome.Mmusculus.UCSC.mm10'.
I would appreciate it.
Dips

> Date: Sun, 7 Sep 2014 19:38:43 +0100
> From: rainmansr at gmail.com
> To: anand.deepti at outlook.com
> CC: bioconductor at r-project.org
> Subject: Re: [BioC] Motif enrichment analysis: Error in transfac format and background frequencies from BSGenome
> 
> 
> Dear Deepti,
> 
> If you want to use the mouse MotifDB motifs you can retrieve them in the 
> correct format for PWMEnrich here:
> 
> http://bioconductor.org/packages/2.14/data/experiment/html/PWMEnrich.Mmusculus.background.html
> 
> Cheers, Robert
> 
> On 07/09/14 16:47, deepti anand wrote:
> > Hi all,
> > I am scanning a geneset for all the Mmusculus motifs and comparing their enrichment to genomic background. I am using MotifDb package to retrieve motifs and PWMEnrich for doing motif enrichment. I am getting error in the below code-
> >
> > 1). Get all motifs in Mmusculus from MotifDb in transfac format-
> > In this step when exporting the motifs as TRANSFAC format I am getting error. Here are my codes:
> >
> >
> >> motifs.denovo = query(MotifDb, 'Mmusculus')
> >> export(motifs.denovo,con='MotifDBFile',format='transfac')
> > Error in cat(list(...), file, sep, fill, labels, append) :
> >    argument 1 (type 'closure') cannot be handled by 'cat'
> >
> >
> >   
> > 2). Convert count matrices into PWMs: In this step the error is in getting the background frequencies from Mmusculus BSgenome. Here are my code:
> >
> >
> >> library(BSgenome.Mmusculus.UCSC.mm10)
> >>   genome = BSgenome.Mmusculus.UCSC.mm10
> >> genomic.acgt = getBackgroundFrequencies("BSgenome.Mmusculus.UCSC.mm10")
> > Error in pickGenome(organism) :
> >    Please pick one of the valid organisms: "dm3" or provide a BSgenome object of the target genome.
> >
> >
> > I would appreciate any help
> >
> >
> > Dips 		 	   		
> > 	[[alternative HTML version deleted]]
> >
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