I was hoping someone could please help explain how RPKM values are calculated using the MEDIPS package?
From the source code (v1.16) it says RPKM values are calculated the following way:
I am assuming that genome_count(Set) is referring to "number of reads detected in each bin" and that window_size it the bin size. However, I am a bit unsure what number_regions(Set) refers to? Is that the number of windows generated for the reference genome or something else? And how does this compare/deviate from calculating the RPKM values by dividing the genome_count*10^9 with the total read count (sum(genome_count(Set)))
Also, does anyone know whether the strategy for calculating RPKM values has changes between MEDIPS versions (fx. between v1.6 and v1.16)?