[Repitools-help] Repitools-Question about gcContent argument of cpgBoxplots function

Guillaume Devailly devailly at lyon.fnclcc.fr
Thu Jul 21 12:33:07 CEST 2011

Hello everyone,
I am a France PhD student working in epigenetic. I am currently working 
on ChIP on chip data we produced using affymetrix human promoter 1.0R 
arrays. I am currently dicovering Repitools which seems very usefull!

I want to do a CpG BoxPlot of my data to see if my favorite protein 
binding sites are dependant of CpG density. It seems that the function 
cpgBoxplots can do such things, so I decided to try it.
In the help pages of this function, it is said that about the gcContent 
A  range of GC content, which only probes that have GC content in the 
range are  used for the graphing.
The default value seems to be: gcContent=7:18

However, when I do that, it plot a first graph with a probe G+C content 
of 7, then it erase and plot another graph with a probe G+C content of 
8,  then 9, 10, 11, ... and finally 18, whereas I intended to do a 
single graph with all the probes containing a C+G content between 7 and 
Am I doing it the wrong way ? Is gcContent function can do such a thing 

Thank you very much for your help.
Best regards,

Guillaume DEVAILLY
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