Packages

case class EnrichedDbnsfp(chromosome: String = "1", start: String = "69897", reference: String = "T", alternate: String = "C", aaref: Option[String] = None, symbol: String = "SLC35A3", ensembl_gene_id: String = "ENSG00000117620", ensembl_protein_id: String = "ENSP00000491146", VEP_canonical: String = ".", ensembl_transcript_id: String = "ENST00000450305", cds_strand: String = "+", SIFT_score: Option[Double] = None, SIFT_pred: Option[String] = None, SIFT_converted_rankscore: Option[Double] = None, Polyphen2_HDIV_score: Option[Double] = None, Polyphen2_HDIV_pred: Option[String] = None, Polyphen2_HDIV_rankscore: Option[Double] = None, Polyphen2_HVAR_score: Option[Double] = None, Polyphen2_HVAR_pred: Option[String] = None, Polyphen2_HVAR_rankscore: Option[Double] = None, FATHMM_score: Option[Double] = None, FATHMM_pred: Option[String] = None, FATHMM_converted_rankscore: Option[Double] = None, CADD_raw: Double = 5.734485, CADD_raw_rankscore: Double = 0.95178, CADD_phred: Double = 34.0, DANN_score: Double = 0.9947908619510818, DANN_rankscore: Double = 0.66795, REVEL_rankscore: Option[Double] = None, REVEL_score: Option[Double] = None, LRT_converted_rankscore: Option[Double] = None, LRT_pred: Option[String] = None, LRT_score: Option[Double] = None, phyloP100way_vertebrate: Double = 8.947, phyloP100way_vertebrate_rankscore: Double = 0.92735, phyloP30way_mammalian: Double = 1.312, phyloP30way_mammalian_rankscore: Double = 0.94714, phyloP17way_primate: Double = 0.756, phyloP17way_primate_rankscore: Double = 0.94297, phastCons100way_vertebrate: Double = 1.0, phastCons100way_vertebrate_rankscore: Double = 0.71638, phastcons30way_mammalian: Double = 0.998, phastCons30way_mammalian_rankscore: Double = 0.65909, phastCons17way_primate: Double = 0.986, phastCons17way_primate_rankscore: Double = 0.61781, GERP++_NR: Double = 4.76, GERP++_RS: Double = 4.76, GERP++_RS_rankscore: Double = 0.60189, MutPred_rankscore: Option[Double] = None, MutPred_score: Option[Double] = None, MutationAssessor_pred: Option[String] = None, MutationAssessor_score: Option[Double] = None, MutationAssessor_rankscore: Option[Double] = None, MutationTaster_converted_rankscore: Double = 0.81001, PROVEAN_pred: Option[String] = None, PROVEAN_score: Option[Double] = None, PROVEAN_converted_rankscore: Option[Double] = None, VEST4_score: Option[Double] = None, VEST4_rankscore: Option[Double] = None, MetaSVM_pred: Option[String] = None, MetaSVM_rankscore: Option[Double] = None, MetaSVM_score: Option[Double] = None, MetaLR_pred: Option[String] = None, MetaLR_rankscore: Option[Double] = None, MetaLR_score: Option[Double] = None, M-CAP_pred: Option[String] = None, M-CAP_score: Option[Double] = None, M-CAP_rankscore: Option[Double] = None, MPC_score: Option[Double] = None, MPC_rankscore: Option[Double] = None, MVP_score: Option[Double] = None, MVP_rankscore: Option[Double] = None, PrimateAI_pred: Option[String] = None, PrimateAI_rankscore: Option[Double] = None, PrimateAI_score: Option[Double] = None, DEOGEN2_pred: Option[String] = None, DEOGEN2_score: Option[Double] = None, DEOGEN2_rankscore: Option[Double] = None, BayesDel_addAF_pred: String = "D", BayesDel_addAF_rankscore: Double = 0.99412, BayesDel_addAF_score: Double = 0.625005, BayesDel_noAF_pred: String = "D", BayesDel_noAF_rankscore: Double = 0.99401, BayesDel_noAF_score: Double = 0.66, ClinPred_pred: Option[String] = None, ClinPred_rankscore: Option[Double] = None, ClinPred_score: Option[Double] = None, LIST-S2_pred: Option[String] = None, LIST-S2_score: Option[Double] = None, LIST-S2_rankscore: Option[Double] = None, fathmm-MKL_coding_pred: String = "D", fathmm-MKL_coding_rankscore: Double = 0.99037, fathmm-MKL_coding_score: Double = 0.99731, fathmm-MKL_coding_group: String = "AEFBI", fathmm-XF_coding_pred: Option[String] = None, fathmm-XF_coding_rankscore: Option[Double] = None, fathmm-XF_coding_score: Option[Double] = None, Eigen-PC-phred_coding: Double = 14.34762, Eigen-PC-raw_coding: Double = 0.913652959600594, Eigen-PC-raw_coding_rankscore: Double = 0.9614, Eigen-phred_coding: Double = 16.85858, Eigen-raw_coding: Double = 1.08438139196827, Eigen-raw_coding_rankscore: Double = 0.97834, GenoCanyon_rankscore: Double = 0.4628, GenoCanyon_score: Double = 0.999922961798521, integrated_confidence_value: Double = 0.0, integrated_fitCons_rankscore: Double = 0.02776, integrated_fitCons_score: Double = 0.106106, GM12878_confidence_value: Double = 0.0, GM12878_fitCons_rankscore: Double = 0.03286, GM12878_fitCons_score: Double = 0.105846, H1-hESC_confidence_value: Double = 0.0, H1-hESC_fitCons_rankscore: Double = 0.0272, H1-hESC_fitCons_score: Double = 0.083675, HUVEC_confidence_value: Double = 0.0, HUVEC_fitCons_rankscore: Double = 0.03346, HUVEC_fitCons_score: Double = 0.109871, LINSIGHT: Double = 0.863041, LINSIGHT_rankscore: Double = 0.53035, bStatistic: Double = 820.0, bStatistic_converted_rankscore: Double = 0.40914, Interpro_domain: String = ".", GTEx_V8_gene: Option[List[String]] = None, GTEx_V8_tissue: Option[List[String]] = None) extends Product with Serializable

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  1. EnrichedDbnsfp
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Instance Constructors

  1. new EnrichedDbnsfp(chromosome: String = "1", start: String = "69897", reference: String = "T", alternate: String = "C", aaref: Option[String] = None, symbol: String = "SLC35A3", ensembl_gene_id: String = "ENSG00000117620", ensembl_protein_id: String = "ENSP00000491146", VEP_canonical: String = ".", ensembl_transcript_id: String = "ENST00000450305", cds_strand: String = "+", SIFT_score: Option[Double] = None, SIFT_pred: Option[String] = None, SIFT_converted_rankscore: Option[Double] = None, Polyphen2_HDIV_score: Option[Double] = None, Polyphen2_HDIV_pred: Option[String] = None, Polyphen2_HDIV_rankscore: Option[Double] = None, Polyphen2_HVAR_score: Option[Double] = None, Polyphen2_HVAR_pred: Option[String] = None, Polyphen2_HVAR_rankscore: Option[Double] = None, FATHMM_score: Option[Double] = None, FATHMM_pred: Option[String] = None, FATHMM_converted_rankscore: Option[Double] = None, CADD_raw: Double = 5.734485, CADD_raw_rankscore: Double = 0.95178, CADD_phred: Double = 34.0, DANN_score: Double = 0.9947908619510818, DANN_rankscore: Double = 0.66795, REVEL_rankscore: Option[Double] = None, REVEL_score: Option[Double] = None, LRT_converted_rankscore: Option[Double] = None, LRT_pred: Option[String] = None, LRT_score: Option[Double] = None, phyloP100way_vertebrate: Double = 8.947, phyloP100way_vertebrate_rankscore: Double = 0.92735, phyloP30way_mammalian: Double = 1.312, phyloP30way_mammalian_rankscore: Double = 0.94714, phyloP17way_primate: Double = 0.756, phyloP17way_primate_rankscore: Double = 0.94297, phastCons100way_vertebrate: Double = 1.0, phastCons100way_vertebrate_rankscore: Double = 0.71638, phastcons30way_mammalian: Double = 0.998, phastCons30way_mammalian_rankscore: Double = 0.65909, phastCons17way_primate: Double = 0.986, phastCons17way_primate_rankscore: Double = 0.61781, GERP++_NR: Double = 4.76, GERP++_RS: Double = 4.76, GERP++_RS_rankscore: Double = 0.60189, MutPred_rankscore: Option[Double] = None, MutPred_score: Option[Double] = None, MutationAssessor_pred: Option[String] = None, MutationAssessor_score: Option[Double] = None, MutationAssessor_rankscore: Option[Double] = None, MutationTaster_converted_rankscore: Double = 0.81001, PROVEAN_pred: Option[String] = None, PROVEAN_score: Option[Double] = None, PROVEAN_converted_rankscore: Option[Double] = None, VEST4_score: Option[Double] = None, VEST4_rankscore: Option[Double] = None, MetaSVM_pred: Option[String] = None, MetaSVM_rankscore: Option[Double] = None, MetaSVM_score: Option[Double] = None, MetaLR_pred: Option[String] = None, MetaLR_rankscore: Option[Double] = None, MetaLR_score: Option[Double] = None, M-CAP_pred: Option[String] = None, M-CAP_score: Option[Double] = None, M-CAP_rankscore: Option[Double] = None, MPC_score: Option[Double] = None, MPC_rankscore: Option[Double] = None, MVP_score: Option[Double] = None, MVP_rankscore: Option[Double] = None, PrimateAI_pred: Option[String] = None, PrimateAI_rankscore: Option[Double] = None, PrimateAI_score: Option[Double] = None, DEOGEN2_pred: Option[String] = None, DEOGEN2_score: Option[Double] = None, DEOGEN2_rankscore: Option[Double] = None, BayesDel_addAF_pred: String = "D", BayesDel_addAF_rankscore: Double = 0.99412, BayesDel_addAF_score: Double = 0.625005, BayesDel_noAF_pred: String = "D", BayesDel_noAF_rankscore: Double = 0.99401, BayesDel_noAF_score: Double = 0.66, ClinPred_pred: Option[String] = None, ClinPred_rankscore: Option[Double] = None, ClinPred_score: Option[Double] = None, LIST-S2_pred: Option[String] = None, LIST-S2_score: Option[Double] = None, LIST-S2_rankscore: Option[Double] = None, fathmm-MKL_coding_pred: String = "D", fathmm-MKL_coding_rankscore: Double = 0.99037, fathmm-MKL_coding_score: Double = 0.99731, fathmm-MKL_coding_group: String = "AEFBI", fathmm-XF_coding_pred: Option[String] = None, fathmm-XF_coding_rankscore: Option[Double] = None, fathmm-XF_coding_score: Option[Double] = None, Eigen-PC-phred_coding: Double = 14.34762, Eigen-PC-raw_coding: Double = 0.913652959600594, Eigen-PC-raw_coding_rankscore: Double = 0.9614, Eigen-phred_coding: Double = 16.85858, Eigen-raw_coding: Double = 1.08438139196827, Eigen-raw_coding_rankscore: Double = 0.97834, GenoCanyon_rankscore: Double = 0.4628, GenoCanyon_score: Double = 0.999922961798521, integrated_confidence_value: Double = 0.0, integrated_fitCons_rankscore: Double = 0.02776, integrated_fitCons_score: Double = 0.106106, GM12878_confidence_value: Double = 0.0, GM12878_fitCons_rankscore: Double = 0.03286, GM12878_fitCons_score: Double = 0.105846, H1-hESC_confidence_value: Double = 0.0, H1-hESC_fitCons_rankscore: Double = 0.0272, H1-hESC_fitCons_score: Double = 0.083675, HUVEC_confidence_value: Double = 0.0, HUVEC_fitCons_rankscore: Double = 0.03346, HUVEC_fitCons_score: Double = 0.109871, LINSIGHT: Double = 0.863041, LINSIGHT_rankscore: Double = 0.53035, bStatistic: Double = 820.0, bStatistic_converted_rankscore: Double = 0.40914, Interpro_domain: String = ".", GTEx_V8_gene: Option[List[String]] = None, GTEx_V8_tissue: Option[List[String]] = None)

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. val BayesDel_addAF_pred: String
  5. val BayesDel_addAF_rankscore: Double
  6. val BayesDel_addAF_score: Double
  7. val BayesDel_noAF_pred: String
  8. val BayesDel_noAF_rankscore: Double
  9. val BayesDel_noAF_score: Double
  10. val CADD_phred: Double
  11. val CADD_raw: Double
  12. val CADD_raw_rankscore: Double
  13. val ClinPred_pred: Option[String]
  14. val ClinPred_rankscore: Option[Double]
  15. val ClinPred_score: Option[Double]
  16. val DANN_rankscore: Double
  17. val DANN_score: Double
  18. val DEOGEN2_pred: Option[String]
  19. val DEOGEN2_rankscore: Option[Double]
  20. val DEOGEN2_score: Option[Double]
  21. val Eigen-PC-phred_coding: Double
  22. val Eigen-PC-raw_coding: Double
  23. val Eigen-PC-raw_coding_rankscore: Double
  24. val Eigen-phred_coding: Double
  25. val Eigen-raw_coding: Double
  26. val Eigen-raw_coding_rankscore: Double
  27. val FATHMM_converted_rankscore: Option[Double]
  28. val FATHMM_pred: Option[String]
  29. val FATHMM_score: Option[Double]
  30. val GERP++_NR: Double
  31. val GERP++_RS: Double
  32. val GERP++_RS_rankscore: Double
  33. val GM12878_confidence_value: Double
  34. val GM12878_fitCons_rankscore: Double
  35. val GM12878_fitCons_score: Double
  36. val GTEx_V8_gene: Option[List[String]]
  37. val GTEx_V8_tissue: Option[List[String]]
  38. val GenoCanyon_rankscore: Double
  39. val GenoCanyon_score: Double
  40. val H1-hESC_confidence_value: Double
  41. val H1-hESC_fitCons_rankscore: Double
  42. val H1-hESC_fitCons_score: Double
  43. val HUVEC_confidence_value: Double
  44. val HUVEC_fitCons_rankscore: Double
  45. val HUVEC_fitCons_score: Double
  46. val Interpro_domain: String
  47. val LINSIGHT: Double
  48. val LINSIGHT_rankscore: Double
  49. val LIST-S2_pred: Option[String]
  50. val LIST-S2_rankscore: Option[Double]
  51. val LIST-S2_score: Option[Double]
  52. val LRT_converted_rankscore: Option[Double]
  53. val LRT_pred: Option[String]
  54. val LRT_score: Option[Double]
  55. val M-CAP_pred: Option[String]
  56. val M-CAP_rankscore: Option[Double]
  57. val M-CAP_score: Option[Double]
  58. val MPC_rankscore: Option[Double]
  59. val MPC_score: Option[Double]
  60. val MVP_rankscore: Option[Double]
  61. val MVP_score: Option[Double]
  62. val MetaLR_pred: Option[String]
  63. val MetaLR_rankscore: Option[Double]
  64. val MetaLR_score: Option[Double]
  65. val MetaSVM_pred: Option[String]
  66. val MetaSVM_rankscore: Option[Double]
  67. val MetaSVM_score: Option[Double]
  68. val MutPred_rankscore: Option[Double]
  69. val MutPred_score: Option[Double]
  70. val MutationAssessor_pred: Option[String]
  71. val MutationAssessor_rankscore: Option[Double]
  72. val MutationAssessor_score: Option[Double]
  73. val MutationTaster_converted_rankscore: Double
  74. val PROVEAN_converted_rankscore: Option[Double]
  75. val PROVEAN_pred: Option[String]
  76. val PROVEAN_score: Option[Double]
  77. val Polyphen2_HDIV_pred: Option[String]
  78. val Polyphen2_HDIV_rankscore: Option[Double]
  79. val Polyphen2_HDIV_score: Option[Double]
  80. val Polyphen2_HVAR_pred: Option[String]
  81. val Polyphen2_HVAR_rankscore: Option[Double]
  82. val Polyphen2_HVAR_score: Option[Double]
  83. val PrimateAI_pred: Option[String]
  84. val PrimateAI_rankscore: Option[Double]
  85. val PrimateAI_score: Option[Double]
  86. val REVEL_rankscore: Option[Double]
  87. val REVEL_score: Option[Double]
  88. val SIFT_converted_rankscore: Option[Double]
  89. val SIFT_pred: Option[String]
  90. val SIFT_score: Option[Double]
  91. val VEP_canonical: String
  92. val VEST4_rankscore: Option[Double]
  93. val VEST4_score: Option[Double]
  94. val aaref: Option[String]
  95. val alternate: String
  96. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  97. val bStatistic: Double
  98. val bStatistic_converted_rankscore: Double
  99. val cds_strand: String
  100. val chromosome: String
  101. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  102. val ensembl_gene_id: String
  103. val ensembl_protein_id: String
  104. val ensembl_transcript_id: String
  105. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  106. val fathmm-MKL_coding_group: String
  107. val fathmm-MKL_coding_pred: String
  108. val fathmm-MKL_coding_rankscore: Double
  109. val fathmm-MKL_coding_score: Double
  110. val fathmm-XF_coding_pred: Option[String]
  111. val fathmm-XF_coding_rankscore: Option[Double]
  112. val fathmm-XF_coding_score: Option[Double]
  113. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  114. val integrated_confidence_value: Double
  115. val integrated_fitCons_rankscore: Double
  116. val integrated_fitCons_score: Double
  117. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  118. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  119. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  120. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  121. val phastCons100way_vertebrate: Double
  122. val phastCons100way_vertebrate_rankscore: Double
  123. val phastCons17way_primate: Double
  124. val phastCons17way_primate_rankscore: Double
  125. val phastCons30way_mammalian_rankscore: Double
  126. val phastcons30way_mammalian: Double
  127. val phyloP100way_vertebrate: Double
  128. val phyloP100way_vertebrate_rankscore: Double
  129. val phyloP17way_primate: Double
  130. val phyloP17way_primate_rankscore: Double
  131. val phyloP30way_mammalian: Double
  132. val phyloP30way_mammalian_rankscore: Double
  133. val reference: String
  134. val start: String
  135. val symbol: String
  136. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  137. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  138. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  139. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated
    Deprecated

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