compute genome composition (total amount of introns/exons etc)

Question

[jenyka_dm]

Hi, Following chip-seq analysis, the distribution of peaks over chromosome regions was computed using chippeakanno (assignChromosomeRegion). Now, I am trying to find out the actual composition of the genome (the total of amount of exons, introns, intergenic regions etc). Any suggestions on how I can get that info using chippeakanno (I need the same parameters that were used initially to define the regions)? Looking for the Arabidopsis thaliana genome. Thank you!!!!

Answer 1

[aditi.qamra]

You can parse the TxDb object you used for this genome to annotate the peaks in the first place. See http://genomicsclass.github.io/book/pages/bioc1_annoOverview.html