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 [[alternative HTML version deleted]]

take a look to the pdf() or png() functions, for example pdf("out.pdf") ....plot code.... dev.off() Regards, Oscar El 05/12/2011, a las 13:35, Stefanie Ververs <stefanie.ververs@fh- stralsund.de=""> escribió: > 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 > [[alternative HTML version deleted]]