How to get the all the overlap information of a peak in ChIPseeker

Question

[afli]

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!

[Nitin Narwade]

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

[afli]

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

Answer 1

[Guangchuang Yu]

peakAnno@detailGenomicAnnotation

[afli]

Thank you I got it!

features = attributes(peakAnno)

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

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