Question: Coerce several Granges objects to a GrangeList
0
gravatar for patrick.schordert
5.1 years ago by
United States
patrick.schordert30 wrote:

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 • 755 views
ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by patrick.schordert30
Answer: Coerce several Granges objects to a GrangeList
1
gravatar for James W. MacDonald
5.1 years ago by
United States
James W. MacDonald51k wrote:

Hi Patrick,

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

Best,

Jim

ADD COMMENTlink written 5.1 years ago by James W. MacDonald51k
Answer: Coerce several Granges objects to a GrangeList
0
gravatar for patrick.schordert
5.1 years ago by
United States
patrick.schordert30 wrote:

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!

 

ADD COMMENTlink written 5.1 years ago by patrick.schordert30

Maybe ChIPseeker is helpful?

ADD REPLYlink written 5.1 years ago by Martin Morgan ♦♦ 23k

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.

ADD REPLYlink written 5.1 years ago by patrick.schordert30

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.

ADD REPLYlink written 5.1 years ago by Hervé Pagès ♦♦ 14k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 203 users visited in the last hour