Question: How to get the all the overlap information of a peak in ChIPseeker
0
gravatar for afli
10 months ago by
afli170
China, Beijing, IGDB
afli170 wrote:

Hi guys, I think there must be all the annotation information of one peak in ChIPseeker analysis, for example, a peak could overlap with an exon or an intron. But when I look into the annotation file using as.GRanges method, I could only see one feature corresponding to one peak. I use this command line:

anno<-as.data.frame(as.GRanges(peakAnno))

write.table(anno,"anno.txt",sep="\t",quote=F)

Maybe there is other files that storing all the information? How to get this? Thanks!

ADD COMMENTlink modified 10 months ago • written 10 months ago by afli170

overlap-of-peaks-and-annotated-genes section given in ChIPseeker manual may help you.

ADD REPLYlink written 10 months ago by Nitin Narwade380

Thank you my friend, and I found another answer below.

ADD REPLYlink written 10 months ago by afli170
1
gravatar for Guangchuang Yu
10 months ago by
Guangchuang Yu2.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu2.1k wrote:

peakAnno@detailGenomicAnnotation

ADD COMMENTlink written 10 months ago by Guangchuang Yu2.1k

Thank you I got it!

features = attributes(peakAnno)

head(features['detailGenomicAnnotation'][[1]])

the link is: https://github.com/GuangchuangYu/ChIPseeker/issues/43

ADD REPLYlink modified 10 months ago • written 10 months ago by afli170
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