Class Gtex

  • All Implemented Interfaces:
    java.lang.Iterable<GtexExperiment>

    public class Gtex
    extends java.lang.Object
    implements java.lang.Iterable<GtexExperiment>
    Load data from GTEx files. References: http://www.broadinstitute.org/gtex/
    Author:
    pcingola
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String NA_VALUE  
    • Constructor Summary

      Constructors 
      Constructor Description
      Gtex()  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.util.Collection<java.lang.String> getGeneIds()  
      int getIndex​(java.lang.String geneId)  
      java.util.Iterator<GtexExperiment> iterator()  
      void load​(java.lang.String samples, java.lang.String data)  
      protected void loadData​(java.lang.String data)
      Load data: Experimental (sometimes normalized) values
      protected void loadSamples​(java.lang.String samples)
      Load samples names
      void setVerbose​(boolean verbose)  
      java.lang.String toString()  
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
      • Methods inherited from interface java.lang.Iterable

        forEach, spliterator
    • Constructor Detail

      • Gtex

        public Gtex()
    • Method Detail

      • getGeneIds

        public java.util.Collection<java.lang.String> getGeneIds()
      • getIndex

        public int getIndex​(java.lang.String geneId)
      • load

        public void load​(java.lang.String samples,
                         java.lang.String data)
      • loadData

        protected void loadData​(java.lang.String data)
        Load data: Experimental (sometimes normalized) values
        Parameters:
        data -
      • loadSamples

        protected void loadSamples​(java.lang.String samples)
        Load samples names
        Parameters:
        samples -
      • setVerbose

        public void setVerbose​(boolean verbose)
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object