I was confused about the argument of tssRegion in peak annotation function of ChIPseeker. It seems that there is no change of the annotation output when I changed the tssRegion setting, from tssRegion=c(-3000, 3000) to tssRegion=c(-2000, 0). I am working on a plant species, Brachypodium distachyon (~272 Mb). I thought this is to define the promoter region, which supposed to be upstream of TSS or 5UTR and setting upstream=3000, downstream=3000 is just for plotting around TSS. So, what is the point of this argument here?

And, does anyone know how the promoter was defined in genomic annotation categories (promoter, 5/3 UTR, exon, intron, downstream, intergenic)? For downstream, does it start after 3' UTR? Can I manually set the downstream range, e.g. 500bp?

peakAnno <- annotatePeak(files[[4]], tssRegion=c(-3000, 3000), TxDb=txdb)

Thanks

do you have any reproducible example of change the `tssRegion` setting has no effect of the result?

Figured it out. The problem is the priority of the genomic annotation. Using the priority of ​genomicAnnotationPriority = c( "5UTR",  "Exon", "Intron", "3UTR", "Promoter", "Downstream","Intergenic") gives me same result with tssRegion=c(-3000, 3000)​ or tssRegion=c(-2000, 0)​. But if I change it to genomicAnnotationPriority = c( "Promoter", "5UTR",  "Exon", "Intron", "3UTR",  "Downstream","Intergenic"), it gives me quite different annotation and the annotation (genomicAnnotationPriority = c( "Promoter", "5UTR",  "Exon", "Intron", "3UTR",  "Downstream","Intergenic"), tssRegion=c(-2000, 0)​​) makes more sense in my case.