Package | Description |
---|---|
de.jstacs.sequenceScores.statisticalModels.differentiable |
Provides all
DifferentiableStatisticalModel s, which can compute the gradient with
respect to their parameters for a given input Sequence . |
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous |
Provides
DifferentiableStatisticalModel s that are homogeneous, i.e. |
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif |
Modifier and Type | Method and Description |
---|---|
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 . |
Modifier and Type | Class and Description |
---|---|
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.
|
Constructor and Description |
---|
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 . |