PositionMatrix
Namespace: GibbsSampling
Consists of functions to work with Position-Frequancy-, -Probability- and -WeightMatrices.
Nested types and modules
| Type | Description |
| PositionFrequencyMatrix |
Matrix with fixed positions for nucleotides and amino acids with default value of 0. |
| PositionProbabilityMatrix |
Matrix with fixed positions for nucleotides and amino acids with default value of 0. . |
| PositionWeightMatrix |
Functions and values
| Function or value | Description |
calculateSegmentScoreBy (...)
Signature: pwMatrix:PositionWeightMatrix -> bioItems:(type) -> float
Type parameters: '?7996 |
Calculate the score of the given sequence based on the Probabilities of the PositionWeightMatrix. |
createPFMOf source
Signature: source:(type) -> PositionFrequencyMatrix
Type parameters: '?7976 |
Create PositionFrequencyMatrix based on BioArray. |
createPositionWeightMatrix (...)
Signature: alphabet:'?7994 [] -> pcv:ProbabilityCompositeVector -> ppMatrix:PositionProbabilityMatrix -> PositionWeightMatrix
Type parameters: '?7994 |
Create PositionWeightMatrix based on ProbabilityCompositeVector and PositionProbabilityMatrix. |
createPPMOf positionFrequencyMatrix
Signature: positionFrequencyMatrix:PositionFrequencyMatrix -> PositionProbabilityMatrix
|
Create new PositionWeightMatrix based on existing PositionFrequencyMatrix. The counts of each position of each element are transformed to floats. |
fusePositionFrequencyMatrices (...)
Signature: motiveLength:int -> countMatrices:PositionFrequencyMatrix [] -> PositionFrequencyMatrix
|
Create new PositionFrequencyMatrix based on the sum of the positions of an array of Countmatrices. |
getBestInformationContent item
Signature: item:(float * int) [] [] -> (float * int) []
|
Finds the best information content in an array of arrays of PWMSs and positions. |
increaseInPlacePFM (...)
Signature: pos:int -> bioItem:'a -> positionFrequencyMatrix:PositionFrequencyMatrix -> PositionFrequencyMatrix
Type parameters: 'a |
Increase counter of PositionFrequencyMatrix at fixed position by 1. |
increaseInPlacePFMBy (...)
Signature: pos:int -> bioItem:'a -> n:int -> positionFrequencyMatrix:PositionFrequencyMatrix -> PositionFrequencyMatrix
Type parameters: 'a |
Increase counter of PositionFrequencyMatrix at fixed position by n. |
increaseInPlacePPM (...)
Signature: pos:int -> bioItem:'a -> positionProbabilityMatrix:PositionProbabilityMatrix -> PositionProbabilityMatrix
Type parameters: 'a |
Increase counter of PositionProbabilityMatrix at fixed position by 1. |
increaseInPlacePPMBy (...)
Signature: pos:int -> bioItem:'a -> n:float -> positionProbabilityMatrix:PositionProbabilityMatrix -> PositionProbabilityMatrix
Type parameters: 'a |
Increase counter of PositionProbabilityMatrix at fixed position by n. |
increaseInPlacePWM (...)
Signature: pos:int -> bioItem:'a -> positionWeightMatrix:PositionWeightMatrix -> PositionWeightMatrix
Type parameters: 'a |
Increase counter of PositionWeightMatrix at fixed position by 1. |
increaseInPlacePWMBy (...)
Signature: bioItem:'a -> pos:int -> n:float -> positionWeightMatrix:PositionWeightMatrix -> PositionWeightMatrix
Type parameters: 'a |
|
normalizePPM (...)
Signature: sourceCount:int -> alphabet:'?7986 [] -> pseudoCount:float -> positionFrequencyMatrix:PositionProbabilityMatrix -> PositionProbabilityMatrix
Type parameters: '?7986 |
The counts of each position of each element are transformed to floats. |
