Coerce several Granges objects to a GrangeList
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@patrickschordert-6745
Last seen 7.9 years ago
United States

Hi,

I have three GRanges objects that I am trying to coerce into a GRangesList to feed to the enrichmentPlot() function found in the Repitools package. The final goal is to align my ChIPseq peaks to features like TSSs or enhancers.

Any help is welcomed. Thanks!

GRanges GRangesList ChIP • 1.1k views
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@james-w-macdonald-5106
Last seen 13 hours ago
United States

Hi Patrick,

Have you looked at the help page for GRangesList? If so, is there something unclear that we should correct?

Best,

Jim

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@patrickschordert-6745
Last seen 7.9 years ago
United States

Hi Jim,

Sorry, I got it and tried to delete the post, but didn't find how. It was a 'stupid' question. Just wrote GRangesList(GRange1, GRange2).

I'm trying align some ChIPseq data to TSSs and am following the "A collection of ChIP-seq analyses tools' pdf from Mark Robinson (June 22, 2013). It is strange how such a widespread analysis isn't yet found in a 'simple' package. Would you know of anything out there that I could look into for these kind of things?

Thanks!

 

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Maybe ChIPseeker is helpful?

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Thanks, but I would rather stick with one environment (R). Otherwise, my brains are going to pop out of my skull. I just find it hard to believe that there is nothing out there given it is such a widespread method. Thanks for any help,

p.

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Patrick,

Did you click on the link Martin gave you for ChIPseeker? If you do so you will realize that ChIPseeker is a Bioconductor package. And you are aware that Bioconductor is based on R right? ;-)

H.

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