Package ru.autosome.commons.backgroundModel.mono

Examples of ru.autosome.commons.backgroundModel.mono.WordwiseBackground

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public class PrecalculateThresholdLists extends ru.autosome.ape.cli.generalized.PrecalculateThresholdLists<PWM, BackgroundModel> {

  @Override
  protected void initialize_default_background() {
    background = new WordwiseBackground();
  }
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     "number of recognized words: " + info.numberOfRecognizedWords(background, pwmLength) + "\n------------\n");
  }

  public static void main(String[] args) {
    PWM pwm = new PWMImporter().loadMotif("test_data/pwm/KLF4_f2.pwm");
    BackgroundModel background = new WordwiseBackground();
    Discretizer discretizer = new Discretizer(10000.0);
    Integer max_hash_size = null;
    double threshold = 3;
    double[] thresholds = {3,5,7};
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                         "number of recognized words: " + info.numberOfRecognizedWords(background, pwmLength) + "\n------------\n");
  }

  public static void main(String[] args) {
    PWM pwm = new PWMImporter().loadMotif("test_data/pwm/KLF4_f2.pwm");
    BackgroundModel background = new WordwiseBackground();
    Discretizer discretizer = new Discretizer(10000.0);
    BoundaryType pvalue_boundary = BoundaryType.LOWER;
    Integer max_hash_size = null;
    double pvalue = 0.0005;
    double[] pvalues = {0.0001, 0.0005, 0.001};
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    System.out.println(pwm.score(word));
    System.out.println(dipwm.score(word));

    //DiPWM dipwm_2 = new DiPWMImporter().loadMotif("test_data/dipwm/AP2A.di"));

    run_mono_and_di(pwm, new WordwiseBackground(), discretizer, max_hash_size, threshold);
    run_mono_and_di(pwm, new Background(new double[] {0.1, 0.4, 0.4, 0.1}), discretizer, max_hash_size, threshold);
    run_mono_and_di(pwm, new Background(new double[] {0.25, 0.25, 0.25, 0.25}), discretizer, max_hash_size, threshold);
  }
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Related Classes of ru.autosome.commons.backgroundModel.mono.WordwiseBackground

  • ru.autosome.ape.example.FindPvalue
  • ru.autosome.ape.example.FindPvalueDinucleotide
  • ru.autosome.ape.example.FindThreshold
  • ru.autosome.ape.FindPvalue
  • ru.autosome.ape.FindThreshold
  • ru.autosome.ape.PrecalculateThresholdLists
  • ru.autosome.commons.converter.mono.PCM2PWM
  • ru.autosome.commons.motifModel.mono.PWM
  • ru.autosome.macroape.CollectDistanceMatrix
  • ru.autosome.macroape.EvalSimilarity
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