To plot broadpeak signal in R

[Herty LIANY (GIS)]

Hi,

 

Does anyone know how to plot the ENCODE broadpeak signal (raw data) using R?

i.e. ENCODE broadpeak data:

chr1     798256 798454 .       116      .       4.89716 3.70716 -1

chr1     799435 799507 .       103      .       2.46426 1.54117 -1

 

Desired outcome plot:

 

 

I suppose we shouldn’t use the density function in R? am I right? I really hope someone can share their experience with me?

Thank you very much J

 

Best Regards,

Herty

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[Pauline Fujita]

Hello Herty,

If you are wanting to draw graphs of signal data from ENCODE, you probably want to use the ENCODE uniform signals which are in bigWig format. These are available from the ENCODE downloads page:

encodeproject.org/ENCODE/downloads.html

You may also find our documentation on ENCODE file formats useful:

http://encodeproject.org/FAQ/FAQformat.html#ENCODE

As far as R packages are concerned, unfortunately that is beyond the scope of this list. There are quite a few packages available online, you will have to see which best fits your needs. A good starting point might be the bioconductor site:

http://www.bioconductor.org/help/search/index.html?q=R

Best of luck with your research! If you have further questions regarding Genome Browser usage, please feel free to contact the mailing list again at gen...@soe.ucsc.edu.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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