[BioC] RE : RE : occurrence of rGADEM motifs

[Simon Noël]

 Sory for the last mail, I hit the wrong buton

Simon Noël
CdeC
________________________________________
De : bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] de la part de Simon Noël [simon.noel.2 at ulaval.ca]
Date d'envoi : 26 juillet 2011 13:12
À : mattia pelizzola; bioconductor
Objet : [BioC] RE :  occurrence of rGADEM motifs

Vous en pensez quoi?  En plus, ça utilise Jaspar, une base de donnée très performante et complète que nous n'utilisons âs encore.

Simon Noël
CdeC
________________________________________
De : bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] de la part de mattia pelizzola [mattia.pelizzola at gmail.com]
Date d'envoi : 26 juillet 2011 06:51
À : bioconductor
Objet : [BioC] occurrence of rGADEM motifs

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.
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

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