Hi,
Assuming I have a BED file containing the positions of some peaks on the genome,
I would like to use R calculate the relative distribution of these peaks in the 5'UTR, 3'UTR, and CDS regions of transcripts.
I know ChipSeeker offer a function plotPeakProf2() can provide similar results, such as those mentioned in its documents.
We improved and developed several functions to plot body region of Gene/Transcript/Exon/Intron/3UTR/5UTR. If users want to get more information from the body region, we added upstream and downstream parameters to functions in order to get flank extension of body regions. upstream and downstream can be NULL(default), rel object and actual numbers. NULL(default) reflects body regions with no flank extension. Rel object reflects the percentage of total length of body regions. Actual numbers reflects the actual length of flank extension.
plotPeakProf2(peak = peak, upstream = rel(0.2), downstream = rel(0.2), conf = 0.95, by = "gene", type = "body", nbin = 800, TxDb = txdb, weightCol = "V5",ignore_strand = F)
But this is somewhat different from what I want, as I hope to focus on the CDS region and its upstream and downstream UTRs. I don't know if there are any packages that can do this?
