Package ru.autosome.commons.model

Examples of ru.autosome.commons.model.Discretizer

137
138
139
140
141
142
143
144
145
146
147
    }
  }

  protected void initialize_defaults() {
    initialize_default_background();
    discretizer = new Discretizer(100.0);
    max_hash_size = 10000000;

    dataModel = DataModel.PWM;
    effectiveCount = 100;
    thresholds_folder = null;
View Full Code Here
17
18
19
20
21
22
23
24
25
26
27
  }

  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};

    FindPvalueAPE calculator = new FindPvalueAPE<PWM, BackgroundModel>(pwm, background, discretizer, max_hash_size);
View Full Code Here
19
20
21
22
23
24
25
26
27
28
29
  }

  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};
View Full Code Here
48
49
50
51
52
53
54
55
56
57
58
  }

  public static void main(String[] args) {
    PWM pwm = new PWMImporter().loadMotif("test_data/pwm/KLF4_f2.pwm");

    Discretizer discretizer = new Discretizer(10000.0);
    Integer max_hash_size = null;
    double threshold = 7;
//    double[] thresholds = {3,5,7};

    Sequence word = new Sequence("ACAGTGACAA");
View Full Code Here
TOP

Related Classes of ru.autosome.commons.model.Discretizer

  • ru.autosome.ape.cli.generalized.FindPvalue
  • ru.autosome.ape.cli.generalized.FindThreshold
  • ru.autosome.ape.cli.generalized.PrecalculateThresholdLists
  • ru.autosome.ape.example.FindPvalue
  • ru.autosome.ape.example.FindPvalueDinucleotide
  • ru.autosome.ape.example.FindThreshold
  • ru.autosome.commons.motifModel.di.DiPWM
  • ru.autosome.commons.motifModel.mono.PWM
  • ru.autosome.macroape.cli.generalized.CollectDistanceMatrix
  • ru.autosome.macroape.cli.generalized.EvalSimilarity
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.