Packages

case class DuplexYieldMetric(fraction: Proportion, read_pairs: Count, cs_families: Count, ss_families: Count, ds_families: Count, ds_duplexes: Count, ds_fraction_duplexes: Proportion, ds_fraction_duplexes_ideal: Proportion) extends Metric with Product with Serializable

Metrics produced by CollectDuplexSeqMetrics that are sampled at various levels of coverage, via random downsampling, during the construction of duplex metrics. The downsampling is done in such a way that the fractions are approximate, and not exact, therefore the fraction field should only be interpreted as a guide and the read_pairs field used to quantify how much data was used.

See FamilySizeMetric for detailed definitions of CS, SS and DS as used below.

fraction

The approximate fraction of the full dataset that was used to generate the remaining values.

read_pairs

The number of read pairs upon which the remaining metrics are based.

cs_families

The number of _CS_ (Coordinate & Strand) families present in the data.

ss_families

The number of _SS_ (Single-Strand by UMI) families present in the data.

ds_families

The number of _DS_ (Double-Strand by UMI) families present in the data.

ds_duplexes

The number of _DS_ families that had the minimum number of observations on both strands to be called duplexes (default = 1 read on each strand).

ds_fraction_duplexes

The fraction of _DS_ families that are duplexes (ds_duplexes / ds_families).

ds_fraction_duplexes_ideal

The fraction of _DS_ families that should be duplexes under an idealized model where each strand, A and B, have equal probability of being sampled, given the observed distribution of _DS_ family sizes.

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  1. DuplexYieldMetric
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Instance Constructors

  1. new DuplexYieldMetric(fraction: Proportion, read_pairs: Count, cs_families: Count, ss_families: Count, ds_families: Count, ds_duplexes: Count, ds_fraction_duplexes: Proportion, ds_fraction_duplexes_ideal: Proportion)

    fraction

    The approximate fraction of the full dataset that was used to generate the remaining values.

    read_pairs

    The number of read pairs upon which the remaining metrics are based.

    cs_families

    The number of _CS_ (Coordinate & Strand) families present in the data.

    ss_families

    The number of _SS_ (Single-Strand by UMI) families present in the data.

    ds_families

    The number of _DS_ (Double-Strand by UMI) families present in the data.

    ds_duplexes

    The number of _DS_ families that had the minimum number of observations on both strands to be called duplexes (default = 1 read on each strand).

    ds_fraction_duplexes

    The fraction of _DS_ families that are duplexes (ds_duplexes / ds_families).

    ds_fraction_duplexes_ideal

    The fraction of _DS_ families that should be duplexes under an idealized model where each strand, A and B, have equal probability of being sampled, given the observed distribution of _DS_ family sizes.

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  1. type Self = Iterable[(String, String)]
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  3. def +(other: String): String
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    This member is added by an implicit conversion from DuplexYieldMetric to any2stringadd[DuplexYieldMetric] performed by method any2stringadd in scala.Predef.
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  7. def ->[B](y: B): (DuplexYieldMetric, B)
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  26. def count(p: ((String, String)) ⇒ Boolean): Int
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  27. val cs_families: Count
  28. def drop(n: Int): Iterable[(String, String)]
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  29. def dropRight(n: Int): Iterable[(String, String)]
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  30. def dropWhile(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]
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  31. val ds_duplexes: Count
  32. val ds_families: Count
  33. val ds_fraction_duplexes: Proportion
  34. val ds_fraction_duplexes_ideal: Proportion
  35. def ensuring(cond: (DuplexYieldMetric) ⇒ Boolean, msg: ⇒ Any): DuplexYieldMetric
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    This member is added by an implicit conversion from DuplexYieldMetric to Ensuring[DuplexYieldMetric] performed by method Ensuring in scala.Predef.
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  36. def ensuring(cond: (DuplexYieldMetric) ⇒ Boolean): DuplexYieldMetric
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    This member is added by an implicit conversion from DuplexYieldMetric to Ensuring[DuplexYieldMetric] performed by method Ensuring in scala.Predef.
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  37. def ensuring(cond: Boolean, msg: ⇒ Any): DuplexYieldMetric
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    This member is added by an implicit conversion from DuplexYieldMetric to Ensuring[DuplexYieldMetric] performed by method Ensuring in scala.Predef.
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  38. def ensuring(cond: Boolean): DuplexYieldMetric
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    This member is added by an implicit conversion from DuplexYieldMetric to Ensuring[DuplexYieldMetric] performed by method Ensuring in scala.Predef.
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  52. def formatValue(value: Any): String

    Override this method to customize how values are formatted.

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  53. def formatted(fmtstr: String): String
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  54. val fraction: Proportion
  55. def genericBuilder[B]: Builder[B, Iterable[B]]
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  56. def get(name: String): Option[String]

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

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  57. final def getClass(): Class[_]
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  80. final def ne(arg0: AnyRef): Boolean
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  88. def product[B >: (String, String)](implicit num: Numeric[B]): B
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  89. val read_pairs: Count
  90. def reduce[A1 >: (String, String)](op: (A1, A1) ⇒ A1): A1
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  91. def reduceLeft[B >: (String, String)](op: (B, (String, String)) ⇒ B): B
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  109. def splitAt(n: Int): (Iterable[(String, String)], Iterable[(String, String)])
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  110. val ss_families: Count
  111. def stringPrefix: String
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  112. def sum[B >: (String, String)](implicit num: Numeric[B]): B
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  128. def toMap[T, U](implicit ev: <:<[(String, String), (T, U)]): Map[T, U]
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  129. def toParArray: ParArray[T]
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    (Changed in version 2.9.0) transpose throws an IllegalArgumentException if collections are not uniformly sized.

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

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  140. def view(from: Int, until: Int): IterableView[(String, String), Iterable[(String, String)]]
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  147. 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
    IterableLike → GenIterableLike
  148. def zipWithIndex[A1 >: (String, String), That](implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, Int), That]): That
    Definition Classes
    IterableLike → GenIterableLike
  149. def →[B](y: B): (DuplexYieldMetric, B)
    Implicit
    This member is added by an implicit conversion from DuplexYieldMetric to ArrowAssoc[DuplexYieldMetric] 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 DuplexYieldMetric 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:
    (duplexYieldMetric: 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 DuplexYieldMetric 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:
    (duplexYieldMetric: 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 DuplexYieldMetric 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:
    (duplexYieldMetric: 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 DuplexYieldMetric 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:
    (duplexYieldMetric: MonadOps[(String, String)]).withFilter(p)
    Definition Classes
    MonadOps

Deprecated Value Members

  1. 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 DuplexYieldMetric to CollectionsHaveToParArray[DuplexYieldMetric, T]

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

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

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

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

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

Inherited by implicit conversion alternateImplicit from DuplexYieldMetric to ForceImplicitAmbiguity

Ungrouped