[BioC] occurrence of rGADEM motifs

Heidi Dvinge heidi at ebi.ac.uk
Tue Jul 26 14:12:54 CEST 2011

Hi Mattia,

> Hi,
> I am using rGADEM and MotIV to find out enriched motifs in my ChIPseq
> peaks
> and determine the similarity with Jaspar TFBS. These tools look very
> useful!
> rGADEM provides a list of enriched motifs. The total number of motifs is
> provided by the nOccurrences function, but I can't find a way to get to
> know
> which peak regions do contain these motifs. In particular, what are the
> startPos and endPos functions supposed to do? I would expect a set of
> genomic positions (or positions relative to the peak regions) with the
> same
> length as nOccurrences, but I only get one number for each motif, with no
> chromosome associated.

I don't really know rGADEM, so I can't tell you if there's a direct way of
doing that. You can however extract the PWM itself using getPWM (rGADEM),
and then match it to your sequence(s) of interest with matchPWM
(Biostrings). The latter will also let you control the score, i.e. how
similar the found motif should be to your PWM of interest.

I seem to remember that rGADEM sometimes gives you quite long motifs,
where the information content around the edges is quite low. If you
extract the actual PWMs you might therefore want to consider trimming them
before matching to your sequences.


> Even in the rGADEM vignette you have nOccurrences equal to 60 but then you
> get only one number out of the startPos and endPos functions. Am I missing
> or misunderstanding anything?
> Additionally, I was also wondering if it is possible to control the max
> number of processors used in the analysis. I am working on a cluster
> shared
> between many people and apparently the software uses as many processors as
> possible, while I do not want to be that greedy with other users ..
> Thanks for any hint,
> mattia
> 	[[alternative HTML version deleted]]
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