Just to add on to my question.
In Voila view html file, we can adjust
the threshold of the dPSI and confidence and get the corresponding number of entries (LVS). So what I am really wondering is that how those enteries are validated to fulfill the threshold requirement? The following is my guessing:
From the tsv file generated from voila tsv, each entry/LSV has the columns 'mean_dpsi_per_lsv_junction', 'probability_changing', and 'probability_non_changing'. For one entry/LSV, if its 'mean_dpsi_per_lsv_junction' has at least one value larger than dPSI threshold and its 'probability changing' also has at least one value larger than confidence, is it counted?
I used R to compute a tsv file using my own data and setted threshold, but the result is not consistent with the number counted from voila.
Really appreciate it if I can get some explanations. Or is there any public source code that I can access to?
Looking forward to your reply.