Question: ChIPseeker: Is it possible to create heatmaps / metagene plots without being centered on the TSS?
0
gravatar for cguzman.roma
4.2 years ago by
United States
cguzman.roma0 wrote:

So if you look at https://bioconductor.riken.jp/packages/3.2/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html you will notice that most of the data generated is centered on the TSS. 

 

I would like to know if it is possible to center metagene plots (and other data) either at the start of exons / introns / or exon/intron junctions or in the middle of exons themselves?

I am aware that exons all vary in length so that any firm known middle of the exon does not exist, but perhaps there is a way to normalize exon length throughout the hg19 genome?

Is there anything similar to the TSS but for exons? Introns? Junctions?

 

Thank you!

ADD COMMENTlink modified 4.2 years ago by Guangchuang Yu1.1k • written 4.2 years ago by cguzman.roma0
Answer: ChIPseeker: Is it possible to create heatmaps / metagene plots without being cen
1
gravatar for Guangchuang Yu
4.2 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

Yes, it's possible. getPromoters function is center all peaks to the TSS. This is gene level, I can modify it to intron or exon level.

 

ADD COMMENTlink written 4.2 years ago by Guangchuang Yu1.1k

When you say "I can modify it to intron or exon level" you mean .. you as the developer and then push out an update that would allow us to do this or this is something I can accomplish at this moment too?

Probably a silly question but oh well.

 

Thanks a ton,

ADD REPLYlink written 4.2 years ago by cguzman.roma0

Yes, I am the developer and will work it out in the following day. see the issue https://github.com/GuangchuangYu/ChIPseeker/issues/16

ADD REPLYlink written 4.1 years ago by Guangchuang Yu1.1k

already done.

 

If you have any suggestion, pls comment on the github issue.

ADD REPLYlink written 4.1 years ago by Guangchuang Yu1.1k
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