/useful

Some useful scripts for parsing files

Primary LanguageR

Some useful scripts for parsing files

Replace NAs: Analyze NAs in VAST-TOOLS INCLUSION final Table:

  • 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

How to run:

  • 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)