Package ru.autosome.commons.motifModel.mono

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

9
10
11
12
13
14
15
    super();
  }

  @Override
  protected PPM createMotif(double[][] matrix, String name) {
    return new PPM(matrix, name);
  }
View Full Code Here
68
69
70
71
72
73
74
75
76
77
78
79
                             {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
40
41
42
43
44
45
46
47
48
49
50
    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:
View Full Code Here
TOP

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

  • ru.autosome.commons.converter.mono.PCM2PPM
  • ru.autosome.commons.importer.PWMImporter
  • 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.