• We count how many NAs contain a quality score for every PSI value computed. If they have more than 3, we replace this PSI value with NAnew3.

• Input is the default vast-tools table (INCLUSION-...)

• Output: desired output, script 1: only replacing NAnew3

• If INCLUSION table was produced using last version of vast-tools, we can replace Intron Retention PSI value with NAI if the adjusted pvalue for the "read umbalance" is below 0.05.

• Input is the default vast-tools table (INCLUSION-...)

• Output: desired output, script 1: replacing NAnew3+NAI

• 1.- Download scripts in your desired folder.
• 2.- Load libraries:

library(data.table) library(stringr)

• 3.- Source the function you want to use:

• source("replaceNA.R") # only NewNAs

• source("replaceNAI.R") # NewNAs + NAIs

• Define the input / output files:

• INCFile<-"test.tab"

• OUTFile<-"test_NA_NewN3.tab"

• OUTFile2<-"test_NA_NewN3_NAIs.tab"

• replaceNA(INCFile, OUTFile)

• replaceNAI(INCFile, OUTFile2)