How the optimal peaks are chosen?

[yeroslaviz]

running chipr on my data set returned 361 peaks which were then filtered to only 42 "optimal" peaks.

 $head expt1-2-3_bowtie2_all.bed 
chromosome      2714624 2714865 primary_peak_223        1000    .       14.160550       0.0000000425562058      0.0000360025501378
chromosome      1285217 1285525 primary_peak_107        1000    .       13.369130       0.0000011627957752      0.0004918626129123
chromosome      345522  345762  primary_peak_20 1000    .       10.964530       0.0000130289580002      0.0036741661560522
chromosome      4069970 4070240 primary_peak_347        1000    .       10.339020       0.0000544316372019      0.0115122912681954
pX       871     2718    primary_peak_357        1000    .       6.946890        0.0001101967412251      0.0155377405127344
chromosome      3271118 3271329 primary_peak_262        1000    .       9.168750        0.0003944703809117      0.0417152427814112

$head expt1-2-3_bowtie2_optimal.bed 
chromosome      149828  150004  primary_peak_4  713     .       6.252030        0.0190814211111566      0.3565806113461553
chromosome      345522  345762  primary_peak_20 1000    .       10.964530       0.0000130289580002      0.0036741661560522
chromosome      472281  472521  primary_peak_21 1000    .       8.436970        0.0017831789550360      0.0942855872475306
chromosome      943815  943965  primary_peak_49 374     .       14.850350       0.1256622895285242      0.9582093245621612
chromosome      944293  944463  primary_peak_50 667     .       3.817930        0.0247321095225195      0.3736315117152060

Based on what filtering thresholds/calculation is this done? Somehow I can see peaks with much better p-/q-values in the *all.bed file then I find afterwards in the *optimal.bed file.

Is there a way to see the values calculated for the filtering by the binomial test?

thanks

Assa