@tacazares The "maxatac peaks" example given in peaks.md is missing several of the purportedly required arguments. For example, cutoff_value, cutoff-type and cutoff_file are not specified (I think these are actually optional, given assumed maxatac_data structure and max f1-score default). In addition the command includes an undocumented argument "threshold". Please review!
Also, you might put cutoff_type before cutoff_value, and mention that the range of acceptable cutoff values depends on the cutoff type (precision, recall f1-score range 0-1, and >0 is the only reasonable option for log2FC).
People might not know what log2FC refers to. Please define as log2 (precision / precision_random)
For "maxatac peaks", I bet more people will use this function for prediction versus benchmarking. For that reason, I wonder if it might be better to make the --bin_size default maxATAC resolution 32bp.
@tacazares The "maxatac peaks" example given in peaks.md is missing several of the purportedly required arguments. For example, cutoff_value, cutoff-type and cutoff_file are not specified (I think these are actually optional, given assumed maxatac_data structure and max f1-score default). In addition the command includes an undocumented argument "threshold". Please review!