Accessary programs

There are few accessary programs provided along with the package which might be helpful during the analysis of enhancers.

• Plot size distribution of enhancers:

  Rscript plot_size_distribution.R <size_file.txt>
  
  It provides histogram of sizes
  

• Enhancer distribution: see the distribution of enhancers within different states provided by other softwares (e.g.: ChromHMM)

  perl enhancerDistribution.pl --eFile <enhancer bedFile> --l <list (a tab-delimited file with fileName and name of the states)> --temp <tempDir>
  

Overlaps with different categories will be shown on stdout

• Calculate ML measures: If you have predictions from different softwares on the same dataset and you want to compare ML measures provided by each of them, use

  python calculateML_measures.py --data-file <dataFile> --label-column <label indice>
  
  where, datafile is a 2D matrix with Name, class and features columns
  

Note: see /example folder. Visit Calculate ML measures for output

• validationTestSet.py: If you have a test dataset with the information of the classes, then use this program to get the accuracy given by the model on the test dataset.

  Run:: python validationTestSet.py –output-folder <outFolder> –label-column <”class indices”> –feature-columns <”feature indices”> –test_file “test_file.txt” –model_file <ModelFile> –scalar_file <ScalerFile> –save-file “File Prefix” –verbosity 1

Visit Validation dataset for output