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

[Robert Stojnic]

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 		 	   		
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>
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