/PETS-algorithm-

Primary LanguageJava

###Project description

  • this is a project done during the 2015 summer Purdue University MURI program.
  • the aim of the project is to convert the matlab version of the program into a Java one
  • the original file is PETS and the file in matlab will get the score after running.
  • the Java program that I have done is can get exact the same result.
  • I use JAMA as the matrix library

####notice

  • make sure java is install
  • the file of the matlab version should be convert into .csv. Due to the java code can not run a .mat file

####input

  • the original mat data file is
    • adj.mat: matrix for protein-protein interaction. Possible values: -1, 1, 0
    • proteinName.mat: list of protein names
    • drugName.mat: list of drug names
    • drugVector.mat: matrix of drug-target. Each row stands for a drug, each column stands for a protein
    • Rp.mat: Rp scores for all proteins
    • ExpressionER+.mat: expression for all proteins

####output

  • Matlab version

    • After you run drugScore.m, three will be a variable named drugRankingScore in the Matlab workspace. This is how the output looks like.

  • java version of the code will also output the result too and will be the same as the matlab version.

####how to run

  • matlab version

    • Run drugScore.m. This file will call computePETOneDrug.
    • computePETOneDrug is the main engine and need be optimized.

  • java version

    • use the following command line
      • sh run.sh