ABout grp2-grp1_median_dpsi and grp2-grp1_probability_changing in TSV file (after vovoila modulize)

[Shengwei Xiong]

Hello,

I have a question about voila modulize.

After running:

voila modulize build/sg.zarr build/AQR_C.sgc build/AQR_sh.sgc dpsi/AQR_K562_C-sh.dpsicov -d modulized --show-all --keep-constitutive --overwrite --debug

I noticed that the output TSV file contains headers such as:

"dpsi_changing_threshold": 0.2
"dpsi_probability_changing_threshold": 0.95

Does this mean that all splicing events in the TSV are already considered significant?

However, when I examined the grp2-grp1_probability_changing and grp2-grp1_median_dpsi columns in the TSV, very few values were above 0.95. How should I interpret grp2-grp1_probability_changing and grp2-grp1_median_dpsi in this context?

Best,
Shengwei

[San Jewell]

Hi Shengwei, 

In classic dpsi mode: dpsi_changing_threshold is the threshold needed in delta psi in order to consider the junction changing, and dpsi_probability_changing_threshold is the confidence threshold needed to consider the junction changing. In order to be considered changing, both of these must pass. These flags influence the "junction_changing" column (and also the "event_changing" column -- as long as one junction in the event passes these till be true) These headers are provided at the top of output files for ease of organization / recall. 

The rules for dropping events when not using --show-all are different, as shown in the console log, after making modules, the modules will be dropped if these changing thresholds are not passed by at least one junction in the module. This rule drops at the module level (single exit single entry), rather than the event level. However, it's easy to filter on either the junction_changing or event_changing columns if you would like to limit the result set further. 

Let me know if this helps!

-San