object CorrectUmis

Linear Supertypes
AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. CorrectUmis
  2. AnyRef
  3. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Type Members

  1. case class UmiCorrectionMetrics (umi: String, total_matches: Count = 0, perfect_matches: Count = 0, one_mismatch_matches: Count = 0, two_mismatch_matches: Count = 0, other_matches: Count = 0, fraction_of_matches: Proportion = 0, representation: Double = 0) extends Metric with Product with Serializable

    Metrics produced by CorrectUmis regarding the correction of UMI sequences to a fixed set of known UMIs.

    Metrics produced by CorrectUmis regarding the correction of UMI sequences to a fixed set of known UMIs.

    umi

    The corrected UMI sequence (or all Ns for unmatched).

    total_matches

    The number of UMI sequences that matched/were corrected to this UMI.

    perfect_matches

    The number of UMI sequences that were perfect matches to this UMI.

    one_mismatch_matches

    The number of UMI sequences that matched with a single mismatch.

    two_mismatch_matches

    The number of UMI sequences that matched with two mismatches.

    other_matches

    The number of UMI sequences that matched with three or more mismatches.

    fraction_of_matches

    The fraction of all UMIs that matched or were corrected to this UMI.

    representation

    The total_matches for this UMI divided by the _mean_ total_matches for all UMIs.

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. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  6. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  7. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  8. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  9. def findUmiPairsWithinDistance(umis: Seq[String], distance: Int): Seq[(String, String, Int)]

    Finds pairs of UMIs within the given set that are within some edit distance of each other.

    Finds pairs of UMIs within the given set that are within some edit distance of each other.

    umis

    the set of umis to check

    distance

    the maximum edit distance at which to report pairs of UMIs

    returns

    a Seq of three-tuples containing (umi1, umi2, edit_distance)

  10. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  11. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  12. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  13. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  14. final def notify(): Unit
    Definition Classes
    AnyRef
  15. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  16. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  17. def toString(): String
    Definition Classes
    AnyRef → Any
  18. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  19. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  20. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from AnyRef

Inherited from Any

Ungrouped