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bio.ferlab.datalake.testutils.models.raw

RawCosmicMutationSet

case class RawCosmicMutationSet(GENE_NAME: String = "SF3B1", ACCESSION_NUMBER: String = "ENST00000335508.6", ONC_TSG: String = "oncogene", CGC_TIER: String = "1", MUTATION_URL: String = ..., LEGACY_MUTATION_ID: String = "COSM84677", Mutation CDS: String = "c.2098A>G", Mutation AA: String = "p.K700E", AA_MUT_START: String = "700", AA_MUT_STOP: String = "700", SHARED_AA: String = "9", GENOMIC_WT_ALLELE_SEQ: String = "T", GENOMIC_MUT_ALLELE_SEQ: String = "C", AA_WT_ALLELE_SEQ: String = "K", AA_MUT_ALLELE_SEQ: String = "E", Mutation Description CDS: String = "Substitution", Mutation Description AA: String = "Substitution - Missense", ONTOLOGY_MUTATION_CODE: String = "SO:0001583", GENOMIC_MUTATION_ID: String = "COSV59205318", Mutation genome position GRCh37: String = "2:198266834-198266834", Mutation genome position GRCh38: String = "2:197402110-197402110", COSMIC_SAMPLE_TESTED: String = "86821", COSMIC_SAMPLE_MUTATED: String = "699", DISEASE: String = ..., WGS_DISEASE: String = ..., EXAC_AF: String = "0.0002", EXAC_AFR_AF: String = "0.0003", EXAC_AMR_AF: String = "8.69e-05", EXAC_ADJ_AF: String = "0.0002", EXAC_EAS_AF: String = "0.0003", EXAC_FIN_AF: String = "0", EXAC_NFE_AF: String = "0.0003", EXAC_SAS_AF: String = "0", GNOMAD_EXOMES_AF: String = "8.97e-05", GNOMAD_EXOMES_AFR_AF: String = "6.21e-05", GNOMAD_EXOMES_AMR_AF: String = "3.11e-05", GNOMAD_EXOMES_ASJ_AF: String = "0.0003", GNOMAD_EXOMES_EAS_AF: String = "0", GNOMAD_EXOMES_FIN_AF: String = "4.64e-05", GNOMAD_EXOMES_NFE_AF: String = "0.0001", GNOMAD_EXOMES_SAS_AF: String = "6.76e-05", GNOMAD_GENOMES_AF: String = "3.94e-05", GNOMAD_GENOMES_AFR_AF: String = "0", GNOMAD_GENOMES_AMI_AF: String = "0", GNOMAD_GENOMES_AMR_AF: String = "0", GNOMAD_GENOMES_ASJ_AF: String = "0", GNOMAD_GENOMES_EAS_AF: String = "0", GNOMAD_GENOMES_FIN_AF: String = "0", GNOMAD_GENOMES_MID_AF: String = "0", GNOMAD_GENOMES_NFE_AF: String = "8.82e-05", GNOMAD_GENOMES_SAS_AF: String = "0", CLINVAR_CLNSIG: String = ..., CLINVAR_TRAIT: String = ..., GERP++_RS: String = "6.02", MIN_SIFT_SCORE: String = "0.004", MIN_SIFT_PRED: String = "D", DNDS_DISEASE_QVAL_SIG: String = "breast=4.73e-24", MUTATION_SIGNIFICANCE_TIER: String = "2") extends Product with Serializable

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  1. RawCosmicMutationSet
  2. Serializable
  3. Serializable
  4. Product
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Instance Constructors

  1. new RawCosmicMutationSet(GENE_NAME: String = "SF3B1", ACCESSION_NUMBER: String = "ENST00000335508.6", ONC_TSG: String = "oncogene", CGC_TIER: String = "1", MUTATION_URL: String = ..., LEGACY_MUTATION_ID: String = "COSM84677", Mutation CDS: String = "c.2098A>G", Mutation AA: String = "p.K700E", AA_MUT_START: String = "700", AA_MUT_STOP: String = "700", SHARED_AA: String = "9", GENOMIC_WT_ALLELE_SEQ: String = "T", GENOMIC_MUT_ALLELE_SEQ: String = "C", AA_WT_ALLELE_SEQ: String = "K", AA_MUT_ALLELE_SEQ: String = "E", Mutation Description CDS: String = "Substitution", Mutation Description AA: String = "Substitution - Missense", ONTOLOGY_MUTATION_CODE: String = "SO:0001583", GENOMIC_MUTATION_ID: String = "COSV59205318", Mutation genome position GRCh37: String = "2:198266834-198266834", Mutation genome position GRCh38: String = "2:197402110-197402110", COSMIC_SAMPLE_TESTED: String = "86821", COSMIC_SAMPLE_MUTATED: String = "699", DISEASE: String = ..., WGS_DISEASE: String = ..., EXAC_AF: String = "0.0002", EXAC_AFR_AF: String = "0.0003", EXAC_AMR_AF: String = "8.69e-05", EXAC_ADJ_AF: String = "0.0002", EXAC_EAS_AF: String = "0.0003", EXAC_FIN_AF: String = "0", EXAC_NFE_AF: String = "0.0003", EXAC_SAS_AF: String = "0", GNOMAD_EXOMES_AF: String = "8.97e-05", GNOMAD_EXOMES_AFR_AF: String = "6.21e-05", GNOMAD_EXOMES_AMR_AF: String = "3.11e-05", GNOMAD_EXOMES_ASJ_AF: String = "0.0003", GNOMAD_EXOMES_EAS_AF: String = "0", GNOMAD_EXOMES_FIN_AF: String = "4.64e-05", GNOMAD_EXOMES_NFE_AF: String = "0.0001", GNOMAD_EXOMES_SAS_AF: String = "6.76e-05", GNOMAD_GENOMES_AF: String = "3.94e-05", GNOMAD_GENOMES_AFR_AF: String = "0", GNOMAD_GENOMES_AMI_AF: String = "0", GNOMAD_GENOMES_AMR_AF: String = "0", GNOMAD_GENOMES_ASJ_AF: String = "0", GNOMAD_GENOMES_EAS_AF: String = "0", GNOMAD_GENOMES_FIN_AF: String = "0", GNOMAD_GENOMES_MID_AF: String = "0", GNOMAD_GENOMES_NFE_AF: String = "8.82e-05", GNOMAD_GENOMES_SAS_AF: String = "0", CLINVAR_CLNSIG: String = ..., CLINVAR_TRAIT: String = ..., GERP++_RS: String = "6.02", MIN_SIFT_SCORE: String = "0.004", MIN_SIFT_PRED: String = "D", DNDS_DISEASE_QVAL_SIG: String = "breast=4.73e-24", MUTATION_SIGNIFICANCE_TIER: String = "2")

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
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  3. final def ==(arg0: Any): Boolean
    Definition Classes
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  4. val AA_MUT_ALLELE_SEQ: String
  5. val AA_MUT_START: String
  6. val AA_MUT_STOP: String
  7. val AA_WT_ALLELE_SEQ: String
  8. val ACCESSION_NUMBER: String
  9. val CGC_TIER: String
  10. val CLINVAR_CLNSIG: String
  11. val CLINVAR_TRAIT: String
  12. val COSMIC_SAMPLE_MUTATED: String
  13. val COSMIC_SAMPLE_TESTED: String
  14. val DISEASE: String
  15. val DNDS_DISEASE_QVAL_SIG: String
  16. val EXAC_ADJ_AF: String
  17. val EXAC_AF: String
  18. val EXAC_AFR_AF: String
  19. val EXAC_AMR_AF: String
  20. val EXAC_EAS_AF: String
  21. val EXAC_FIN_AF: String
  22. val EXAC_NFE_AF: String
  23. val EXAC_SAS_AF: String
  24. val GENE_NAME: String
  25. val GENOMIC_MUTATION_ID: String
  26. val GENOMIC_MUT_ALLELE_SEQ: String
  27. val GENOMIC_WT_ALLELE_SEQ: String
  28. val GERP++_RS: String
  29. val GNOMAD_EXOMES_AF: String
  30. val GNOMAD_EXOMES_AFR_AF: String
  31. val GNOMAD_EXOMES_AMR_AF: String
  32. val GNOMAD_EXOMES_ASJ_AF: String
  33. val GNOMAD_EXOMES_EAS_AF: String
  34. val GNOMAD_EXOMES_FIN_AF: String
  35. val GNOMAD_EXOMES_NFE_AF: String
  36. val GNOMAD_EXOMES_SAS_AF: String
  37. val GNOMAD_GENOMES_AF: String
  38. val GNOMAD_GENOMES_AFR_AF: String
  39. val GNOMAD_GENOMES_AMI_AF: String
  40. val GNOMAD_GENOMES_AMR_AF: String
  41. val GNOMAD_GENOMES_ASJ_AF: String
  42. val GNOMAD_GENOMES_EAS_AF: String
  43. val GNOMAD_GENOMES_FIN_AF: String
  44. val GNOMAD_GENOMES_MID_AF: String
  45. val GNOMAD_GENOMES_NFE_AF: String
  46. val GNOMAD_GENOMES_SAS_AF: String
  47. val LEGACY_MUTATION_ID: String
  48. val MIN_SIFT_PRED: String
  49. val MIN_SIFT_SCORE: String
  50. val MUTATION_SIGNIFICANCE_TIER: String
  51. val MUTATION_URL: String
  52. val Mutation AA: String
  53. val Mutation CDS: String
  54. val Mutation Description AA: String
  55. val Mutation Description CDS: String
  56. val Mutation genome position GRCh37: String
  57. val Mutation genome position GRCh38: String
  58. val ONC_TSG: String
  59. val ONTOLOGY_MUTATION_CODE: String
  60. val SHARED_AA: String
  61. val WGS_DISEASE: String
  62. final def asInstanceOf[T0]: T0
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  63. def clone(): AnyRef
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  64. final def eq(arg0: AnyRef): Boolean
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  65. final def getClass(): Class[_]
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  66. final def isInstanceOf[T0]: Boolean
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  67. final def ne(arg0: AnyRef): Boolean
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  68. final def notify(): Unit
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  69. final def notifyAll(): Unit
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  70. final def synchronized[T0](arg0: ⇒ T0): T0
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  71. final def wait(arg0: Long, arg1: Int): Unit
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  72. final def wait(arg0: Long): Unit
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  73. final def wait(): Unit
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