I am trying (and failing) to understand what exactly the peak score from HOMER actually is. I read on the HOMER website that it is the "position adjusted reads from initial peak region - reads per position may be limited" which is found here: http://homer.ucsd.edu/homer/ngs/peaks.html#

But this really doesn't answer my question of what it is. What is a position adjusted read, and where does the actual number come from? Any detailed insights would be really appreciated.