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[], tssRegion=c(-3000, 3000), TxDb=txdb)