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

deepti anand anand.deepti at outlook.com
Sun Sep 7 17:47:20 CEST 2014

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

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