Yay, thank you and Martin very much, it worked!

Now I would like to plot the peaks - there is plotPeaks (see it work in 
the example) - but if I run my script on the server, there is no 
graphical output, of course.
Is it possible to print the graph into a file?

On 23.11.2011 13:24, Oscar Flores wrote:
> This are general coding errors.
>
> For else issue, R expects else brackets in the same line. Try changing:
>
> }
> else
> {
>
> for
>
> }else{
>
>
> And the problem with exporting the bed file, I thing that the problem 
> is that you don't have the variable "name" defined in the description 
> attribute
>
> export.bed(peaks, score=NULL, name="Peaks", *description=name*, 
> filepath=outputfile, splitByChrom=FALSE)
>
>
> I hope this fix your problems
>
> Regards
>
> Oscar


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