peaksPerCell parameter for addReproduciblePeakSet()

[mzhibo]

Hi,
I have a question on the peaksPerCell parameters in addReproduciblePeakSet() .
Why peaksPerCell is set to 500 while the maxPeaks is set to 150k. If I understand it correctly, this makes it only keep up to 500 peaks per group. macs2 cutoff for a p or q value would select significant peaks. In addition, the coverage file is generated with similar number of cells by subsampling. I wonder why setting an upper limit of peaksPerCells here. Would this force to drop some true peaks in groups that have a good number of cells (~1k)?
For clusters that all have above 1k cells, what's your recommended value for peaksPerCell? If I set peaksPerCell to NULL, will it just rely on the cutoff threshold?
Thank you
Zhibo

[rcorces]

Sorry - that interpretation is not correct. It is not peaksPerCellGrouping, it is peaksPerCell. If you have peaksPerCell = 500 and your cell grouping has 100 cells, then the maximum number of peaks that grouping could have would be 500*100 or 50,000
As the parameter says, this is to prevent groups with very few cells from contributing lots of peaks

[rcorces]

also peaksPerCell must be an integer, it cannot be NULL

[mzhibo]

Thank you for clarifying!