Question about setting maxReplicates in addGroupCoverages()

[Captain-Pam]

Hi all,

I am generating pseudo-bulk replicates using addGroupCoverages() (https://www.archrproject.com/bookdown/how-does-archr-make-pseudo-bulk-replicates.html). I am not sure how to choose the parameter maxReplicates if I have more samples.

If I set maxReplicates = 5, only a subset of my biological samples are included in the replicates. Does this mean I may miss peaks that appear only in the excluded samples? Should I set maxReplicates equal to the total number of samples in order to capture more peaks, or is there a recommended strategy to balance replicate number and peak discovery?

Any suggestions are worth it！
Thanks