Samples Column in Splicing Results about psichomics

[nuno-agostinho]

Hi @GuoLabUCSD,

Yes, your assumptions are correct. The samples column refers to the number of samples containing enough junction read counts to quantify the event (by default, psichomics only uses samples with at least 10 read counts supporting the event).

You can check which samples are not being used for AS quantification by going to the PSI table and looking at the samples with missing values (NA) for that event. For instance:

# Get PSI values for this event
eventPSI = psi["SE_3_+_13661331_13663275_13663415_13667945_FBLN2", ]

# Get name of samples with missing values
colnames(is.na(eventPSI))

Hope this helps, but feel free to ask me more questions if needed.

Kind regards,
Nuno

[GuoLabUCSD]

Great, this helps! Thanks.

-Regards,
Joseph