Uses of Class
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.HomogeneousDiffSM

Packages that use HomogeneousDiffSM

de.jstacs.sequenceScores.statisticalModels.differentiable	Provides all DifferentiableStatisticalModels, which can compute the gradient with respect to their parameters for a given input Sequence.
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous	Provides DifferentiableStatisticalModels that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif

Uses of HomogeneousDiffSM in de.jstacs.sequenceScores.statisticalModels.differentiable

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable with parameters of type HomogeneousDiffSM

static ExtendedZOOPSDiffSM

DifferentiableStatisticalModelFactory.createZOOPS(int length, DifferentiableStatisticalModel motif, HomogeneousDiffSM bg) This method allows to create a "zero or one occurrence per sequence" (ZOOPS) model that allows to discover binding sites in a DataSet.

Uses of HomogeneousDiffSM in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous

Subclasses of HomogeneousDiffSM in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous

class	HomogeneousMM0DiffSM This scoring function implements a homogeneous Markov model of order zero (hMM(0)) for a fixed sequence length.
class	HomogeneousMMDiffSM This scoring function implements a homogeneous Markov model of arbitrary order for any sequence length.
class	UniformHomogeneousDiffSM This scoring function does nothing.

Uses of HomogeneousDiffSM in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif

Constructors in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif with parameters of type HomogeneousDiffSM

ExtendedZOOPSDiffSM(boolean type, int length, int starts, boolean plugIn, HomogeneousDiffSM bg, DifferentiableStatisticalModel[] motif, DurationDiffSM[] posPrior, boolean plugInBg)
This constructor creates an instance of ExtendedZOOPSDiffSM that allows to have one site of the specified motifs in a Sequence.

ExtendedZOOPSDiffSM(boolean type, int length, int starts, boolean plugIn, HomogeneousDiffSM bg, DifferentiableStatisticalModel motif, DurationDiffSM posPrior, boolean plugInBg)
This constructor creates an instance of ExtendedZOOPSDiffSM that is either an OOPS or a ZOOPS model depending on the chosen type.