Sailent (BioFSharp) | BioFSharp

Sailent Module

Namespace: BioFSharp.Stats
Assembly: BioFSharp.Stats.dll

Types

Type	Description
SailentCharacterization
SailentResult<'a>

Functions and values

Function or value	Description
`compute verbose bootstrapIterations data` Full Usage: `compute verbose bootstrapIterations data` Parameters: verbose : `bool` bootstrapIterations : `int` data : `OntologyItem<float> array` Returns: `SailentResult<float>`	Compute SAILENT (Surprisal AnalysIs EmpiricaL pErmutatioN Test) for the given annotated dataset. This empirical test was initially designed for the biological application of Surprisal Analysis to test the weight distribution of a given bin of annotations is significantly different than a random distribution of the same size given the whole dataset, but it should be applicable to similar types of datasets. Input: - verbose: if true, bootstrap iterations and runtime for bootstrapping is printed - bootstrapIterations: the amount of distributions to sample from the whole dataset to create test distributions for each binsize present in the data - data: annotated dataset (containing ontology items with the associated feature) a SAILENT test returns 3 descriptors for the input data: Absolute descriptor: test distributions and tests are performed on the absolute values of the dataset Negative descriptor: test distributions and tests are performed on the negative values of the dataset only Absolute descriptor: test distributions and tests are performed on the positive values of the dataset only verbose : `bool` bootstrapIterations : `int` data : `OntologyItem<float> array` Returns: `SailentResult<float>`
`computeOfSARes verbose ontologyMap identifiers bootstrapIterations saRes` Full Usage: `computeOfSARes verbose ontologyMap identifiers bootstrapIterations saRes` Parameters: verbose : `bool` ontologyMap : `Map<string, (string * string)[]>` identifiers : `string[]` bootstrapIterations : `int` saRes : `SAResult` Returns: `SailentResult<float>[]`	Compute SAILENT (Surprisal AnalysIs EmpiricaL pErmutatioN Test) for the given Surprisal Analysis result. This empirical test was designed for the biological application of Surprisal Analysis to test the weight distribution of a given bin of annotations is significantly different than a random distribution of the same size given the whole dataset. Input: - verbose: if true, bootstrap iterations and runtime for bootstrapping is printed - ontologyMap: maps identifiers of the data to ontology annotations (can be created using the BioFSharp.BioDB module) - identifiers: a string array containing the annotations of the data at the same index, used as lookup in the ontology map. - bootstrapIterations: the amount of distributions to sample from the whole dataset to create test distributions for each binsize present in the data - saRes: the Surprisal Analysis Result to test a SAILENT test returns 3 descriptors for each constraint of the Surprisal Nalysis result: Absolute descriptor: test distributions and tests are performed on the absolute values of the dataset Negative descriptor: test distributions and tests are performed on the negative values of the dataset only Absolute descriptor: test distributions and tests are performed on the positive values of the dataset only verbose : `bool` ontologyMap : `Map<string, (string * string)[]>` identifiers : `string[]` bootstrapIterations : `int` saRes : `SAResult` Returns: `SailentResult<float>[]`
`computeOfSAResAsync verbose ontologyMap identifiers bootstrapIterations saRes` Full Usage: `computeOfSAResAsync verbose ontologyMap identifiers bootstrapIterations saRes` Parameters: verbose : `bool` ontologyMap : `Map<string, (string * string)[]>` identifiers : `string[]` bootstrapIterations : `int` saRes : `SAResult` Returns: `Async<SailentResult<float>>[]`	Async version of computeOfSARes to use for parallelization (computeOfSAResAsync ( .. ) \|> Async.Parallel \|> Async.RunSynchronously) verbose : `bool` ontologyMap : `Map<string, (string * string)[]>` identifiers : `string[]` bootstrapIterations : `int` saRes : `SAResult` Returns: `Async<SailentResult<float>>[]`
`prepareDataColumn ontologyMap identifiers rawData` Full Usage: `prepareDataColumn ontologyMap identifiers rawData` Parameters: ontologyMap : `Map<string, (string * string)[]>` identifiers : `string[]` rawData : `float[]` Returns: `OntologyItem<float>[]`	utility function to prepare a dataset column for SAILENT characterization. The ontology map can be created by using the BioFSharp.BioDB module. identifiers: a string array containing the annotations of the data at the same index, used as lookup in the ontology map. rawData: feature array of interest, must be same length as annotations. ontologyMap : `Map<string, (string * string)[]>` identifiers : `string[]` rawData : `float[]` Returns: `OntologyItem<float>[]`
`prepareDataset ontologyMap identifiers rawDataset` Full Usage: `prepareDataset ontologyMap identifiers rawDataset` Parameters: ontologyMap : `Map<string, (string * string)[]>` identifiers : `string[]` rawDataset : `float[][]` Returns: `OntologyItem<float>[][]`	utility function to prepare a dataset (in column major form) for SAILENT characterization. The ontology map can be created by using the BioFSharp.BioDB module. identifiers: a string array containing the annotations of the data at the same index, used as lookup in the ontology map. rawData: feature matrix of interest, columns must have same length as identifiers ontologyMap : `Map<string, (string * string)[]>` identifiers : `string[]` rawDataset : `float[][]` Returns: `OntologyItem<float>[][]`