Hi, I'm trying to annotate peaks using annotatepeak (ChIPseeker) There is no problem using default genomicAnnotationPriority

peakAnno <- annotatePeak(files[[1]], tssRegion = c(-1000, 0), TxDb = txdb, level = "transcript", assignGenomicAnnotation = TRUE, genomicAnnotationPriority = c("Promoter", "5UTR", "3UTR", "Exon", "Intron", "Downstream", "Intergenic"), annoDb = "org.At.tair.db", addFlankGeneInfo = FALSE, flankDistance = 5000, sameStrand = FALSE, ignoreOverlap = FALSE, ignoreUpstream = FALSE, ignoreDownstream = FALSE, overlap = "TSS", verbose = TRUE)

However, when I move "Promoter" behind "Intron", promoters are gone from "Genomic Annotation Summary" table. I mean that promoters are not used for annotation and not that "Frequency" is 0.

Have anybody idea how to fix it?

Jakub