Package ru.autosome.commons.motifModel.mono

Examples of ru.autosome.commons.motifModel.mono.PWM

27
28
29
30
31
32
33
    return new WordwiseBackground();
  }

  @Override
  protected PWM createMotif(double[][] matrix, String name) {
    return new PWM(matrix, name);
  }
View Full Code Here
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
                                {10.5, -3.0, 0.0, 0.0},
                                {5.0, 5.0, 5.0, -10.0},
                                {0.0, 0.0, 0.0, 0.0},
                                {-1.0, 10.5, -1.0, 0.0},
                                {0.0, 0.0, 0.0, 2.0} };
    PWM pwm_manual_constructed = new PWM(matrix_cAVNCT, "PWM for cAVNCt consensus sequence (name of PWM)");

    pwmCollection.add(pwm_manual_constructed);

    // PWM from PPM
    double[][] ppm_matrix = { {0.2, 0.4, 0.2, 0.2},
                             {0.9, 0, 0.05, 0.05},
                             {0.3, 0.3, 0.3, 0.1},
                             {0.25, 0.25, 0.25, 0.25},
                             {0, 0.9, 0, 0.1},
                             {0.2, 0.2, 0.2, 0.4} };
    PPM ppm = new PPM(ppm_matrix, "cAVNCt PPM (slightly different from another cAVNCt matrix)");
    PWM pwm_from_ppm = ppm.to_pwm(background, ppm_effective_count);
    pwmCollection.add(pwm_from_ppm);

    //////////////////////////////////////////////////////////////////////////////////////////////////

    // Now we should get collection of SNPs with sequence around them. Each SNP should have only two variants (if one need 3 or 4 variants, it's possible to add several SNPs: 1-2, 2-3, 1-3 for instance)
View Full Code Here
12
13
14
15
16
17
18
19
20
21
22
23
import ru.autosome.macroape.calculation.generalized.CompareModelsCountsGiven;
import ru.autosome.macroape.calculation.mono.CompareModels;

public class EvaluateSimilarity {
  public static void main(String[] args){
    PWM firstPWM = new PWMImporter().loadMotif("test_data/pwm/KLF4_f2.pwm");
    PWM secondPWM = new PWMImporter().loadMotif("test_data/pwm/SP1_f1.pwm");
    try {
      Discretizer discretizer = new Discretizer(100.0);

//      CountingPWM firstPWMCounting = new CountingPWM(firstPWM.discrete(discretizer), new WordwiseBackground(), null);
//      CountingPWM secondPWMCounting = new CountingPWM(secondPWM.discrete(discretizer), new WordwiseBackground(), null);
View Full Code Here
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
  }
 
  // constructs PWM from any source: pwm/pcm/ppm matrix
  @Override
  public PWM createMotif(double matrix[][], String name) {
    PWM pwm;
    switch (dataModel) {
      case PCM:
        pwm = new PCM(matrix, name).to_pwm(background);
        break;
      case PPM:
        pwm = new PPM(matrix, name).to_pwm(background, effectiveCount);
        break;
      case PWM:
        pwm = new PWM(matrix, name);
        break;
      default:
        throw new Error("This code never reached");
    }
    return pwm;
View Full Code Here
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
     "pvalue: " + info.pvalue + "\n" +
     "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};

    FindPvalueAPE calculator = new FindPvalueAPE<PWM, BackgroundModel>(pwm, background, discretizer, max_hash_size);

      // Single threshold
    {
      CanFindPvalue.PvalueInfo info = null;
      try {
        info = calculator.pvalueByThreshold(threshold);
      } catch (HashOverflowException e) {
        e.printStackTrace();
      }
      print_result(info, background, pwm.length());
    }

      // Multiple thresholds
    {
      CanFindPvalue.PvalueInfo[] infos = new CanFindPvalue.PvalueInfo[0];
      try {
        infos = calculator.pvaluesByThresholds(thresholds);
      } catch (HashOverflowException e) {
        e.printStackTrace();
      }
      for (CanFindPvalue.PvalueInfo info : infos) {
        print_result(info, background, pwm.length());
      }
    }

    // api integration
    double[][] matrix_cAVNCT = { {1.0, 2.0, 1.0, 1.0},
                          {10.5, -3.0, 0.0, 0.0},
                          {5.0, 5.0, 5.0, -10.0},
                          {0.0, 0.0, 0.0, 0.0},
                          {-1.0, 10.5, -1.0, 0.0},
                          {0.0, 0.0, 0.0, 2.0}};
    PWM pwm_manual_constructed = new PWM(matrix_cAVNCT, "PWM for cAVNCt consensus sequence");
    double[] thresholds_2 = {15,16,17};
    ru.autosome.ape.api.FindPvalueAPE.Parameters parameters =
     new ru.autosome.ape.api.FindPvalueAPE.Parameters(pwm_manual_constructed,
                                                      thresholds_2,
                                                      discretizer, background, max_hash_size);
    ru.autosome.ape.api.FindPvalueAPE bioumlCalculator = new ru.autosome.ape.api.FindPvalueAPE(parameters);
    CanFindPvalue.PvalueInfo[] infosBiouml = bioumlCalculator.call();
    for (CanFindPvalue.PvalueInfo bioumlInfo : infosBiouml) {
      print_result(bioumlInfo, background, pwm_manual_constructed.length());
    }
  }
View Full Code Here
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
                         "actual pvalue: " + info.real_pvalue + "\n" +
                         "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};

    CanFindThreshold calculator = new FindThresholdAPE<PWM, BackgroundModel>(pwm, background, discretizer, max_hash_size);

    // Single threshold
    {
      CanFindThreshold.ThresholdInfo info = null;
      try {
        info = calculator.thresholdByPvalue(pvalue, pvalue_boundary);
      } catch (HashOverflowException e) {
        e.printStackTrace();
      }
      print_result(info, background, pwm.length());
    }
    // Multiple thresholds
    {
      CanFindThreshold.ThresholdInfo[] infos = new CanFindThreshold.ThresholdInfo[0];
      try {
        infos = calculator.thresholdsByPvalues(pvalues, pvalue_boundary);
      } catch (HashOverflowException e) {
        e.printStackTrace();
      }
      for (CanFindThreshold.ThresholdInfo info : infos) {
        print_result(info, background, pwm.length());
      }
    }
    // api integration
    ru.autosome.ape.api.FindThresholdAPE.Parameters parameters =
     new ru.autosome.ape.api.FindThresholdAPE.Parameters(pwm,
                                                              pvalues,
                                                              background,
                                                              discretizer,pvalue_boundary, max_hash_size);
    ru.autosome.ape.api.FindThresholdAPE bioumlCalculator = new ru.autosome.ape.api.FindThresholdAPE(parameters);
    CanFindThreshold.ThresholdInfo[] infosBiouml = bioumlCalculator.call();
    for (CanFindThreshold.ThresholdInfo bioumlInfo : infosBiouml) {
      print_result(bioumlInfo, background, pwm.length());
    }
  }
View Full Code Here
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
      e.printStackTrace();
    }
  }

  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");
    DiPWM dipwm = DiPWM.fromPWM(pwm); // A way to transform mono-nucleotide to di matrix

    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);
View Full Code Here
TOP

Related Classes of ru.autosome.commons.motifModel.mono.PWM

  • ru.autosome.ape.example.FindPvalue
  • ru.autosome.ape.example.FindPvalueDinucleotide
  • ru.autosome.ape.example.FindThreshold
  • ru.autosome.commons.backgroundModel.mono.WordwiseBackground
  • ru.autosome.commons.converter.mono.PCM2PWM
  • ru.autosome.commons.importer.PWMImporter
  • ru.autosome.commons.model.Discretizer
  • ru.autosome.macroape.example.EvaluateSimilarity
  • ru.autosome.perfectosape.calculation.ScoringModelDistributions.CountingPWM
  • ru.autosome.perfectosape.example.MultiSNPScan
    • 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.