object FirthTest extends LogitTest

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LogitTest, Serializable, Serializable, AnyRef, Any
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Type Members

  1. type FitState = FirthFitState

    Type for the state that the test maintains between variants.

    Type for the state that the test maintains between variants.

    Definition Classes
    FirthTest → LogitTest

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
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  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
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  4. final def asInstanceOf[T0]: T0
    Definition Classes
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  5. def clone(): AnyRef
    Attributes
    protected[java.lang]
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    @native() @throws( ... )
  6. final def eq(arg0: AnyRef): Boolean
    Definition Classes
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  7. def equals(arg0: Any): Boolean
    Definition Classes
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  8. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
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    @throws( classOf[java.lang.Throwable] )
  9. def fitFirth(x: DenseMatrix[Double], y: DenseVector[Double], args: FirthNewtonArgs, maxIter: Int = 100, tol: Double = 1e-6): FirthFit
  10. def fitStatePerPhenotype: Boolean

    If true, the FitState uses per-phenotype information and must be refit for each phenotype.

    If true, the FitState uses per-phenotype information and must be refit for each phenotype. If false, the FitState only depends on the covariates

    Definition Classes
    FirthTest → LogitTest
  11. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  12. def hashCode(): Int
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    @native()
  13. def init(phenotypes: Array[Double], covariates: DenseMatrix): FirthFitState

    Initializes a FitState for a (covariate matrix, phenotype array) pair.

    Initializes a FitState for a (covariate matrix, phenotype array) pair.

    As much memory allocation as possible should be performed in this step to avoid allocations in the per-row fit.

    Definition Classes
    FirthTest → LogitTest
  14. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  15. final def ne(arg0: AnyRef): Boolean
    Definition Classes
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  16. final def notify(): Unit
    Definition Classes
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    @native()
  17. final def notifyAll(): Unit
    Definition Classes
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    @native()
  18. val resultSchema: StructType
    Definition Classes
    FirthTest → LogitTest
  19. def runTest(genotypes: DenseVector[Double], phenotypes: DenseVector[Double], fitState: FirthFitState): InternalRow
    Definition Classes
    FirthTest → LogitTest
  20. def solveUpperTriangular(a: DenseMatrix[Double], b: DenseVector[Double]): DenseVector[Double]
  21. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
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  22. def toString(): String
    Definition Classes
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  23. final def wait(): Unit
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  24. final def wait(arg0: Long, arg1: Int): Unit
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  25. final def wait(arg0: Long): Unit
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Inherited from LogitTest

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