[ChIPSeeker] Getting overlapping genomic feature annotation (e.g. peak locate in gene A & defined TSS region of gene B)

Question

[chiefcat]

Hi guys,

I'm trying to use ChIPseeker but couldn't find a way to call the overlapping features during peak annotation.

Example:

TSS setting: -3kb +500bp

--> I would like to get the ChIP peak annotated with "Rrs1, 3'UTR" & "Adhfe1, TSS" I've tried a lot of different arguments but all of them just me ONLY "Rrs1, 3'UTR"

Do anyone know how to do this?

And If a peak is overlapping with 2 different gene promoters, can ChIPseek annotate this?

Thanks!!

Answer 1

[Guangchuang Yu]

there is a genomicAnnotationPriority parameter documented in https://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html#peak-annotation. You can select to report "Rrs1, 3'UTR" OR "Adhfe1, TSS", but and "Rrs1, 3'UTR" & "Adhfe1, TSS" as annotatePeak only report the 1st hit according to the annotation priority.

Maybe setting the parameter addFlankGeneInfo = TRUE, flankDistance = 1000 will give you some useful information. The above parameters will report a new column of flanking genes with all the genes at the flanking region of the peak (e.g. [-1000, 1000] if flankDistance = 1000).

[helenhuang.math]

Hi Guangchuang, thanks for the suggestion. Adding addFlankGeneInfo and flankDistance is useful to identify all nearby genes.

But is it possible to get the specific annotation information for the flanking genes, for example "Rrs1, 3'UTR" or "exon", "intron"?

Thank you!