Hi mattia,

About the number of processors used: rGADEM is using openMP to speed up
certain parts of the calculation. So in order to control the maximum number
of processor used, one of your option would be to set the OMP_NUM_THREADS
environment variable.

For example, you can write the command "export OMP_NUM_THREADS=8" on a linux
terminal before starting a rGADEM analysis and openMP will only use 8
threads. I do not have access to other operating system right now to test
this, but I found informations on setting the OMP_NUM_THREADS environment
variable in this page:
http://software.intel.com/sites/products/documentation/hpc/composerxe/en-us/cpp/lin/optaps/common/optaps_par_var.htm

Best regards,
Charles Joly Beauparlant.



> 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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