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How does getPromoter( ) function in ChIPseeker retrieve one promoter for each gene and not consider other alternative promoters of different transcripts?
Thanks!
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My intuition is that it returns the "TSS" of the genes table (instead of looking at the transcripts table), that is to say the
start
of + genes or theend
of minus genes. Usually the genes coordinates are inclusive, they include the entire range of all the transcripts, so the gene's TSS would be the most upstream (+ genes) or the most downstream (- genes) transcript TSS.Thanks for your reply. It's very likely the getPromoter function works as you said. When I perform intersection between ChIPseq peaks and promoters, the promoters affect the result. I think it's better to obtain promoters for all transcripts.
Thanks!