ChipSeeker genomic features

Question

[GK1610]

Hi

Does anyone know how promoters, introns, exons , 5utr, 3utr, downstream and distal intergenic regions are quantified or determined for a given set of peak in ChIPseeker package

https://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html

[Santosh Anand]

It is using annotation from R annotation package TxDb.Hsapiens.UCSC.hg19.knownGene , which in turn is based on knownGene of UCSC table ( check uscs table browser and you should get the same annotation)

[GK1610]

Thanks, do you know how it does for distal-intergenic region?I couldn't find that

[Santosh Anand]

My guess will be that it is far from TSS (>3k) of gene. But why do you need this info?