Package org.biojava.nbio.survival.cox

Class SurvivalInfoHelper

java.lang.Object
org.biojava.nbio.survival.cox.SurvivalInfoHelper
public class SurvivalInfoHelper extends Object
Used to work with SurvivalInfo
Author:
Scooter Willis

  • Constructor Details

    • SurvivalInfoHelper

      public SurvivalInfoHelper()

  • Method Details

    • dump

      public static void dump(ArrayList<SurvivalInfo> DataT, PrintStream ps, String delimiter)
      For each analysis this allows outputing of the data used in the calculations to a printstream/file. This then allows the file to be loaded into R and calculations can be verified.
      Parameters:
      DataT -
      ps -
      delimiter -

    • categorizeData

      public static void categorizeData(ArrayList<SurvivalInfo> DataT)
      Take a collection of categorical data and convert it to numeric to be used in cox calculations
      Parameters:
      DataT -

    • addInteraction

      public static ArrayList<String> addInteraction(String variable1, String variable2, ArrayList<SurvivalInfo> survivalInfoList)
      To test for interactions use two variables and create a third variable where the two are multiplied together.
      Parameters:
      variable1 -
      variable2 -
      survivalInfoList -
      Returns:

    • groupByRange

      public static void groupByRange(double[] range, String variable, String groupName, ArrayList<SurvivalInfo> survivalInfoList) throws Exception
      Need to allow a range of values similar to cut in R and a continuous c
      Parameters:
      range -
      variable -
      groupName -
      survivalInfoList -
      Throws:
      Exception

    • getGroupCategories

      public static ArrayList<String> getGroupCategories(String groupName, ArrayList<SurvivalInfo> survivalInfoList)
      Parameters:
      groupName -
      survivalInfoList -
      Returns: