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com.fulcrumgenomics.rnaseq

ErccSummaryMetrics

case class ErccSummaryMetrics(total_reads: Long, ercc_reads: Long, fraction_ercc_reads: Double, ercc_templates: Long, total_transcripts: Int, passing_filter_transcripts: Int, pearsons_correlation: Option[Double], spearmans_correlation: Option[Double], intercept: Option[Double], slope: Option[Double], r_squared: Option[Double]) extends Metric with Product with Serializable

Metrics produced by CollectErccMetrics describing various summary metrics related to the spike-in of ERCC (External RNA Controls Consortium) into an RNA-Seq experiment.

The correlation coefficients and linear regression are calculated based on the log2 observed read pair count normalized by ERCC transcript length versus the log2 expected concentration.

total_reads

the total number of reads considered.

ercc_reads

the total number of reads mapping to an ERCC transcript.

fraction_ercc_reads

the fraction of total reads that map to an ERCC transcript.

ercc_templates

the total number of read pairs (or single end reads) mapping to an ERCC transcript.

total_transcripts

the total number of ERCC transcripts with at least one read observed.

passing_filter_transcripts

the total number of ERCC transcripts with at least the user-set minimum # of reads observed.

pearsons_correlation

Pearson's correlation coefficient for correlation of concentration and normalized counts.

spearmans_correlation

Spearman's correlation coefficient for correlation of concentration and normalized counts.

intercept

the intercept of the linear regression.

slope

the slope of the linear regression.

r_squared

the r-squared of the linear regression.

Linear Supertypes
Serializable, Serializable, Metric, Iterable[(String, String)], IterableLike[(String, String), Iterable[(String, String)]], GenIterable[(String, String)], GenIterableLike[(String, String), Iterable[(String, String)]], Traversable[(String, String)], GenTraversable[(String, String)], GenericTraversableTemplate[(String, String), Iterable], TraversableLike[(String, String), Iterable[(String, String)]], GenTraversableLike[(String, String), Iterable[(String, String)]], Parallelizable[(String, String), ParIterable[(String, String)]], TraversableOnce[(String, String)], GenTraversableOnce[(String, String)], FilterMonadic[(String, String), Iterable[(String, String)]], HasNewBuilder[(String, String), Iterable[(String, String)] @scala.annotation.unchecked.uncheckedVariance], Product, Equals, AnyRef, Any
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  1. ErccSummaryMetrics
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Implicitly
  1. by CollectionsHaveToParArray
  2. by MonadOps
  3. by any2stringadd
  4. by StringFormat
  5. by Ensuring
  6. by ArrowAssoc
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Instance Constructors

  1. new ErccSummaryMetrics(total_reads: Long, ercc_reads: Long, fraction_ercc_reads: Double, ercc_templates: Long, total_transcripts: Int, passing_filter_transcripts: Int, pearsons_correlation: Option[Double], spearmans_correlation: Option[Double], intercept: Option[Double], slope: Option[Double], r_squared: Option[Double])

    total_reads

    the total number of reads considered.

    ercc_reads

    the total number of reads mapping to an ERCC transcript.

    fraction_ercc_reads

    the fraction of total reads that map to an ERCC transcript.

    ercc_templates

    the total number of read pairs (or single end reads) mapping to an ERCC transcript.

    total_transcripts

    the total number of ERCC transcripts with at least one read observed.

    passing_filter_transcripts

    the total number of ERCC transcripts with at least the user-set minimum # of reads observed.

    pearsons_correlation

    Pearson's correlation coefficient for correlation of concentration and normalized counts.

    spearmans_correlation

    Spearman's correlation coefficient for correlation of concentration and normalized counts.

    intercept

    the intercept of the linear regression.

    slope

    the slope of the linear regression.

    r_squared

    the r-squared of the linear regression.

Type Members

  1. type Self = Iterable[(String, String)]
    Attributes
    protected[this]
    Definition Classes
    TraversableLike
  2. class WithFilter extends FilterMonadic[A, Repr]
    Definition Classes
    TraversableLike

Value Members

  1. final def !=(arg0: Any): Boolean
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  2. final def ##(): Int
    Definition Classes
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  3. def +(other: String): String
    Implicit
    This member is added by an implicit conversion from ErccSummaryMetrics to any2stringadd[ErccSummaryMetrics] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ++[B >: (String, String), That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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  5. def ++:[B >: (String, String), That](that: Traversable[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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  6. def ++:[B >: (String, String), That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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    TraversableLike
  7. def ->[B](y: B): (ErccSummaryMetrics, B)
    Implicit
    This member is added by an implicit conversion from ErccSummaryMetrics to ArrowAssoc[ErccSummaryMetrics] performed by method ArrowAssoc in scala.Predef.
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    ArrowAssoc
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    @inline()
  8. final def ==(arg0: Any): Boolean
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  9. def addString(b: StringBuilder): StringBuilder
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  10. def addString(b: StringBuilder, sep: String): StringBuilder
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  11. def addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder
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  12. def aggregate[B](z: ⇒ B)(seqop: (B, (String, String)) ⇒ B, combop: (B, B) ⇒ B): B
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  13. def apply(name: String): String

    Gets the value of the field by name.

    Gets the value of the field by name.

    Definition Classes
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  14. final def asInstanceOf[T0]: T0
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  15. def canEqual(that: Any): Boolean
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  16. def clone(): AnyRef
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    @throws( ... ) @native()
  17. def collect[B, That](pf: PartialFunction[(String, String), B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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  18. def collectFirst[B](pf: PartialFunction[(String, String), B]): Option[B]
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  19. def companion: GenericCompanion[Iterable]
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  20. def copyToArray[B >: (String, String)](xs: Array[B], start: Int, len: Int): Unit
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  21. def copyToArray[B >: (String, String)](xs: Array[B]): Unit
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  22. def copyToArray[B >: (String, String)](xs: Array[B], start: Int): Unit
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  23. def copyToBuffer[B >: (String, String)](dest: Buffer[B]): Unit
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  24. def count(p: ((String, String)) ⇒ Boolean): Int
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  25. def drop(n: Int): Iterable[(String, String)]
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  26. def dropRight(n: Int): Iterable[(String, String)]
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    IterableLike
  27. def dropWhile(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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  28. def ensuring(cond: (ErccSummaryMetrics) ⇒ Boolean, msg: ⇒ Any): ErccSummaryMetrics
    Implicit
    This member is added by an implicit conversion from ErccSummaryMetrics to Ensuring[ErccSummaryMetrics] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  29. def ensuring(cond: (ErccSummaryMetrics) ⇒ Boolean): ErccSummaryMetrics
    Implicit
    This member is added by an implicit conversion from ErccSummaryMetrics to Ensuring[ErccSummaryMetrics] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  30. def ensuring(cond: Boolean, msg: ⇒ Any): ErccSummaryMetrics
    Implicit
    This member is added by an implicit conversion from ErccSummaryMetrics to Ensuring[ErccSummaryMetrics] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  31. def ensuring(cond: Boolean): ErccSummaryMetrics
    Implicit
    This member is added by an implicit conversion from ErccSummaryMetrics to Ensuring[ErccSummaryMetrics] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  32. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  33. val ercc_reads: Long
  34. val ercc_templates: Long
  35. def exists(p: ((String, String)) ⇒ Boolean): Boolean
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    IterableLike → TraversableLike → TraversableOnce → GenTraversableOnce
  36. def filter(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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  37. def filterNot(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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  38. def finalize(): Unit
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    @throws( classOf[java.lang.Throwable] )
  39. def find(p: ((String, String)) ⇒ Boolean): Option[(String, String)]
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  40. def flatMap[B, That](f: ((String, String)) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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  41. def flatten[B](implicit asTraversable: ((String, String)) ⇒ GenTraversableOnce[B]): Iterable[B]
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  42. def fold[A1 >: (String, String)](z: A1)(op: (A1, A1) ⇒ A1): A1
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  43. def foldLeft[B](z: B)(op: (B, (String, String)) ⇒ B): B
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  44. def foldRight[B](z: B)(op: ((String, String), B) ⇒ B): B
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  45. def forall(p: ((String, String)) ⇒ Boolean): Boolean
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  46. def foreach[U](f: ((String, String)) ⇒ U): Unit
    Definition Classes
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  47. def formatValue(value: Any): String

    Override this method to customize how values are formatted.

    Override this method to customize how values are formatted.

    Attributes
    protected
    Definition Classes
    Metric
  48. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from ErccSummaryMetrics to StringFormat[ErccSummaryMetrics] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  49. val fraction_ercc_reads: Double
  50. def genericBuilder[B]: Builder[B, Iterable[B]]
    Definition Classes
    GenericTraversableTemplate
  51. def get(name: String): Option[String]

    Gets the value of the field by name, returns None if it does not exist.

    Gets the value of the field by name, returns None if it does not exist.

    Definition Classes
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  52. final def getClass(): Class[_]
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  53. def groupBy[K](f: ((String, String)) ⇒ K): Map[K, Iterable[(String, String)]]
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  54. def grouped(size: Int): Iterator[Iterable[(String, String)]]
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  55. def hasDefiniteSize: Boolean
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  56. def head: (String, String)
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  57. def headOption: Option[(String, String)]
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  58. def init: Iterable[(String, String)]
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  59. def inits: Iterator[Iterable[(String, String)]]
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  60. val intercept: Option[Double]
  61. def isEmpty: Boolean
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  62. final def isInstanceOf[T0]: Boolean
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  63. final def isTraversableAgain: Boolean
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  64. def iterator: Iterator[(String, String)]

    Gets an iterator over the fields of this metric in the order they were defined.

    Gets an iterator over the fields of this metric in the order they were defined. Returns tuples of names and values

    Definition Classes
    Metric → IterableLike → GenIterableLike
  65. def last: (String, String)
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  66. def lastOption: Option[(String, String)]
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  67. def map[B, That](f: ((String, String)) ⇒ B)(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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    TraversableLike → GenTraversableLike → FilterMonadic
  68. def max[B >: (String, String)](implicit cmp: Ordering[B]): (String, String)
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  69. def maxBy[B](f: ((String, String)) ⇒ B)(implicit cmp: Ordering[B]): (String, String)
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    TraversableOnce → GenTraversableOnce
  70. def min[B >: (String, String)](implicit cmp: Ordering[B]): (String, String)
    Definition Classes
    TraversableOnce → GenTraversableOnce
  71. def minBy[B](f: ((String, String)) ⇒ B)(implicit cmp: Ordering[B]): (String, String)
    Definition Classes
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  72. def mkString: String
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  73. def mkString(sep: String): String
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  74. def mkString(start: String, sep: String, end: String): String
    Definition Classes
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  75. def names: Seq[String]

    Get the names of the arguments in the order they were defined.

    Get the names of the arguments in the order they were defined.

    Definition Classes
    Metric
  76. final def ne(arg0: AnyRef): Boolean
    Definition Classes
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  77. def newBuilder: Builder[(String, String), Iterable[(String, String)]]
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  78. def nonEmpty: Boolean
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  79. final def notify(): Unit
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  80. final def notifyAll(): Unit
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  81. def par: ParIterable[(String, String)]
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  82. def parCombiner: Combiner[(String, String), ParIterable[(String, String)]]
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  83. def partition(p: ((String, String)) ⇒ Boolean): (Iterable[(String, String)], Iterable[(String, String)])
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  84. val passing_filter_transcripts: Int
  85. val pearsons_correlation: Option[Double]
  86. def product[B >: (String, String)](implicit num: Numeric[B]): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
  87. val r_squared: Option[Double]
  88. def reduce[A1 >: (String, String)](op: (A1, A1) ⇒ A1): A1
    Definition Classes
    TraversableOnce → GenTraversableOnce
  89. def reduceLeft[B >: (String, String)](op: (B, (String, String)) ⇒ B): B
    Definition Classes
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  90. def reduceLeftOption[B >: (String, String)](op: (B, (String, String)) ⇒ B): Option[B]
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  91. def reduceOption[A1 >: (String, String)](op: (A1, A1) ⇒ A1): Option[A1]
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  92. def reduceRight[B >: (String, String)](op: ((String, String), B) ⇒ B): B
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  93. def reduceRightOption[B >: (String, String)](op: ((String, String), B) ⇒ B): Option[B]
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  94. def repr: Iterable[(String, String)]
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  95. def reversed: List[(String, String)]
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  96. def sameElements[B >: (String, String)](that: GenIterable[B]): Boolean
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  97. def scan[B >: (String, String), That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[Iterable[(String, String)], B, That]): That
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  98. def scanLeft[B, That](z: B)(op: (B, (String, String)) ⇒ B)(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
    Definition Classes
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  99. def scanRight[B, That](z: B)(op: ((String, String), B) ⇒ B)(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That
    Definition Classes
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    Migration

    (Changed in version 2.9.0) The behavior of scanRight has changed. The previous behavior can be reproduced with scanRight.reverse.

  100. def seq: Iterable[(String, String)]
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  101. def size: Int
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  102. def sizeHintIfCheap: Int
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    protected[collection]
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  103. def slice(from: Int, until: Int): Iterable[(String, String)]
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  104. def sliding(size: Int, step: Int): Iterator[Iterable[(String, String)]]
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  105. def sliding(size: Int): Iterator[Iterable[(String, String)]]
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  106. val slope: Option[Double]
  107. def span(p: ((String, String)) ⇒ Boolean): (Iterable[(String, String)], Iterable[(String, String)])
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  108. val spearmans_correlation: Option[Double]
  109. def splitAt(n: Int): (Iterable[(String, String)], Iterable[(String, String)])
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  110. def stringPrefix: String
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  111. def sum[B >: (String, String)](implicit num: Numeric[B]): B
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  112. final def synchronized[T0](arg0: ⇒ T0): T0
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  113. def tail: Iterable[(String, String)]
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  114. def tails: Iterator[Iterable[(String, String)]]
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  115. def take(n: Int): Iterable[(String, String)]
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  116. def takeRight(n: Int): Iterable[(String, String)]
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  117. def takeWhile(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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  118. def thisCollection: Iterable[(String, String)]
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  119. def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, (String, String), Col[(String, String)]]): Col[(String, String)]
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  120. def toArray[B >: (String, String)](implicit arg0: ClassTag[B]): Array[B]
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  121. def toBuffer[B >: (String, String)]: Buffer[B]
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  122. def toCollection(repr: Iterable[(String, String)]): Iterable[(String, String)]
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  123. def toIndexedSeq: IndexedSeq[(String, String)]
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  124. def toIterable: Iterable[(String, String)]
    Definition Classes
    IterableLike → TraversableOnce → GenTraversableOnce
  125. def toIterator: Iterator[(String, String)]
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    @deprecatedOverriding( ... , "2.11.0" )
  126. def toList: List[(String, String)]
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  127. def toMap[T, U](implicit ev: <:<[(String, String), (T, U)]): Map[T, U]
    Definition Classes
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  128. def toParArray: ParArray[T]
    Implicit
    This member is added by an implicit conversion from ErccSummaryMetrics to CollectionsHaveToParArray[ErccSummaryMetrics, T] performed by method CollectionsHaveToParArray in scala.collection.parallel. This conversion will take place only if an implicit value of type (ErccSummaryMetrics) ⇒ GenTraversableOnce[T] is in scope.
    Definition Classes
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  129. def toSeq: Seq[(String, String)]
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  130. def toSet[B >: (String, String)]: Set[B]
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  131. def toStream: Stream[(String, String)]
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  132. def toString(): String
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  133. def toTraversable: Traversable[(String, String)]
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    @deprecatedOverriding( ... , "2.11.0" )
  134. def toVector: Vector[(String, String)]
    Definition Classes
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  135. val total_reads: Long
  136. val total_transcripts: Int
  137. def transpose[B](implicit asTraversable: ((String, String)) ⇒ GenTraversableOnce[B]): Iterable[Iterable[B]]
    Definition Classes
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    @migration
    Migration

    (Changed in version 2.9.0) transpose throws an IllegalArgumentException if collections are not uniformly sized.

  138. def unzip[A1, A2](implicit asPair: ((String, String)) ⇒ (A1, A2)): (Iterable[A1], Iterable[A2])
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  139. def unzip3[A1, A2, A3](implicit asTriple: ((String, String)) ⇒ (A1, A2, A3)): (Iterable[A1], Iterable[A2], Iterable[A3])
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  140. def values: Seq[String]

    Get the values of the arguments in the order they were defined.

    Get the values of the arguments in the order they were defined.

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  141. def view(from: Int, until: Int): IterableView[(String, String), Iterable[(String, String)]]
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  142. def view: IterableView[(String, String), Iterable[(String, String)]]
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  143. final def wait(): Unit
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  144. final def wait(arg0: Long, arg1: Int): Unit
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  145. final def wait(arg0: Long): Unit
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  146. def withFilter(p: ((String, String)) ⇒ Boolean): FilterMonadic[(String, String), Iterable[(String, String)]]
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  147. def zip[A1 >: (String, String), B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, B), That]): That
    Definition Classes
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  148. def zipAll[B, A1 >: (String, String), That](that: GenIterable[B], thisElem: A1, thatElem: B)(implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, B), That]): That
    Definition Classes
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  149. def zipWithIndex[A1 >: (String, String), That](implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, Int), That]): That
    Definition Classes
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  150. def →[B](y: B): (ErccSummaryMetrics, B)
    Implicit
    This member is added by an implicit conversion from ErccSummaryMetrics to ArrowAssoc[ErccSummaryMetrics] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Shadowed Implicit Value Members

  1. def filter(p: ((String, String)) ⇒ Boolean): TraversableOnce[(String, String)]
    Implicit
    This member is added by an implicit conversion from ErccSummaryMetrics to MonadOps[(String, String)] performed by method MonadOps in scala.collection.TraversableOnce.
    Shadowing
    This implicitly inherited member is shadowed by one or more members in this class.
    To access this member you can use a type ascription:
    (erccSummaryMetrics: MonadOps[(String, String)]).filter(p)
    Definition Classes
    MonadOps
  2. def flatMap[B](f: ((String, String)) ⇒ GenTraversableOnce[B]): TraversableOnce[B]
    Implicit
    This member is added by an implicit conversion from ErccSummaryMetrics to MonadOps[(String, String)] performed by method MonadOps in scala.collection.TraversableOnce.
    Shadowing
    This implicitly inherited member is shadowed by one or more members in this class.
    To access this member you can use a type ascription:
    (erccSummaryMetrics: MonadOps[(String, String)]).flatMap(f)
    Definition Classes
    MonadOps
  3. def map[B](f: ((String, String)) ⇒ B): TraversableOnce[B]
    Implicit
    This member is added by an implicit conversion from ErccSummaryMetrics to MonadOps[(String, String)] performed by method MonadOps in scala.collection.TraversableOnce.
    Shadowing
    This implicitly inherited member is shadowed by one or more members in this class.
    To access this member you can use a type ascription:
    (erccSummaryMetrics: MonadOps[(String, String)]).map(f)
    Definition Classes
    MonadOps
  4. def withFilter(p: ((String, String)) ⇒ Boolean): Iterator[(String, String)]
    Implicit
    This member is added by an implicit conversion from ErccSummaryMetrics to MonadOps[(String, String)] performed by method MonadOps in scala.collection.TraversableOnce.
    Shadowing
    This implicitly inherited member is shadowed by one or more members in this class.
    To access this member you can use a type ascription:
    (erccSummaryMetrics: MonadOps[(String, String)]).withFilter(p)
    Definition Classes
    MonadOps

Deprecated Value Members

  1. def /:[B](z: B)(op: (B, (String, String)) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
    Annotations
    @deprecated
    Deprecated

    (Since version 2.12.10) Use foldLeft instead of /:

  2. def :\[B](z: B)(op: ((String, String), B) ⇒ B): B
    Definition Classes
    TraversableOnce → GenTraversableOnce
    Annotations
    @deprecated
    Deprecated

    (Since version 2.12.10) Use foldRight instead of :\

  3. def formatValues(value: Any): String

    Attributes
    protected
    Definition Classes
    Metric
    Annotations
    @deprecated
    Deprecated

    (Since version 0.5.0) Use formatValue instead.

Inherited from Serializable

Inherited from Serializable

Inherited from Metric

Inherited from Iterable[(String, String)]

Inherited from IterableLike[(String, String), Iterable[(String, String)]]

Inherited from GenIterable[(String, String)]

Inherited from GenIterableLike[(String, String), Iterable[(String, String)]]

Inherited from Traversable[(String, String)]

Inherited from GenTraversable[(String, String)]

Inherited from GenericTraversableTemplate[(String, String), Iterable]

Inherited from TraversableLike[(String, String), Iterable[(String, String)]]

Inherited from GenTraversableLike[(String, String), Iterable[(String, String)]]

Inherited from Parallelizable[(String, String), ParIterable[(String, String)]]

Inherited from TraversableOnce[(String, String)]

Inherited from GenTraversableOnce[(String, String)]

Inherited from FilterMonadic[(String, String), Iterable[(String, String)]]

Inherited from HasNewBuilder[(String, String), Iterable[(String, String)] @scala.annotation.unchecked.uncheckedVariance]

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion CollectionsHaveToParArray from ErccSummaryMetrics to CollectionsHaveToParArray[ErccSummaryMetrics, T]

Inherited by implicit conversion MonadOps from ErccSummaryMetrics to MonadOps[(String, String)]

Inherited by implicit conversion any2stringadd from ErccSummaryMetrics to any2stringadd[ErccSummaryMetrics]

Inherited by implicit conversion StringFormat from ErccSummaryMetrics to StringFormat[ErccSummaryMetrics]

Inherited by implicit conversion Ensuring from ErccSummaryMetrics to Ensuring[ErccSummaryMetrics]

Inherited by implicit conversion ArrowAssoc from ErccSummaryMetrics to ArrowAssoc[ErccSummaryMetrics]

Inherited by implicit conversion alternateImplicit from ErccSummaryMetrics to ForceImplicitAmbiguity

Ungrouped