OntologyEnrichment (BioFSharp) | BioFSharp

OntologyEnrichment Module

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

Types

Type	Description
GseaResult<'a>	Represents a gene set enrichment result
OntologyItem<'a>	Represents an item in an ontology set

Functions and values

Function or value	Description
`CalcHyperGeoPvalue numberOfDEsInBin numberInBin totalUnivers totalNumberOfDE splitPvalueThreshold` Full Usage: `CalcHyperGeoPvalue numberOfDEsInBin numberInBin totalUnivers totalNumberOfDE splitPvalueThreshold` Parameters: numberOfDEsInBin : `int` numberInBin : `int` totalUnivers : `int` totalNumberOfDE : `int` splitPvalueThreshold : `int` Returns: `float`	Calculates p value based on hypergeometric distribution (pValue <= k) numberOfDEsInBin : `int` numberInBin : `int` totalUnivers : `int` totalNumberOfDE : `int` splitPvalueThreshold : `int` Returns: `float`
`CalcOverEnrichment deGroupIndex splitPvalueThreshold minNumberInTerm data` Full Usage: `CalcOverEnrichment deGroupIndex splitPvalueThreshold minNumberInTerm data` Parameters: deGroupIndex : `int` splitPvalueThreshold : `int option` minNumberInTerm : `int option` data : `OntologyItem<'a> seq` Returns: `GseaResult<'a> seq`	Calculates functional term enrichment deGroupIndex : `int` splitPvalueThreshold : `int option` minNumberInTerm : `int option` data : `OntologyItem<'a> seq` Returns: `GseaResult<'a> seq`
`CalcSimpleOverEnrichment deGroupIndex splitPvalueThreshold data` Full Usage: `CalcSimpleOverEnrichment deGroupIndex splitPvalueThreshold data` Parameters: deGroupIndex : `int` splitPvalueThreshold : `int option` data : `OntologyItem<'a> seq` Returns: `GseaResult<'a> seq`	Calculates functional term enrichment deGroupIndex : `int` splitPvalueThreshold : `int option` data : `OntologyItem<'a> seq` Returns: `GseaResult<'a> seq`
`createGseaResult ontologyTerm desInBin numberOfDEsInBin numberInBin totalNumberOfDE totalUnivers pValue` Full Usage: `createGseaResult ontologyTerm desInBin numberOfDEsInBin numberInBin totalNumberOfDE totalUnivers pValue` Parameters: ontologyTerm : `string` desInBin : `OntologyItem<'a> seq` numberOfDEsInBin : `int` numberInBin : `int` totalNumberOfDE : `int` totalUnivers : `int` pValue : `float` Returns: `GseaResult<'a>`	Creates a gene set enrichment result ontologyTerm : `string` desInBin : `OntologyItem<'a> seq` numberOfDEsInBin : `int` numberInBin : `int` totalNumberOfDE : `int` totalUnivers : `int` pValue : `float` Returns: `GseaResult<'a>`
`createOntologyItem id ontologyTerm groupIndex item` Full Usage: `createOntologyItem id ontologyTerm groupIndex item` Parameters: id : `string` ontologyTerm : `string` groupIndex : `int` item : `'a` Returns: `OntologyItem<'a>`	Creates an item in an ontology set id : `string` ontologyTerm : `string` groupIndex : `int` item : `'a` Returns: `OntologyItem<'a>`
`expandOntologyTree data` Full Usage: `expandOntologyTree data` Parameters: data : `OntologyItem<'a> seq` Returns: `OntologyItem<'a> seq`	Extends leaf OntologyEntries to their full tree data : `OntologyItem<'a> seq` Returns: `OntologyItem<'a> seq`
`splitMapManOntologyItemsBy separator data` Full Usage: `splitMapManOntologyItemsBy separator data` Parameters: separator : `char` data : `OntologyItem<'a> seq` Returns: `OntologyItem<'a> seq`	Splits MapMan OntologyEntries with seperator concatenated TermIds Attention: Also parses string to int to get rid of 0 - terms separator : `char` data : `OntologyItem<'a> seq` Returns: `OntologyItem<'a> seq`
`splitMultipleAnnotationsBy separator item` Full Usage: `splitMultipleAnnotationsBy separator item` Parameters: separator : `char` item : `OntologyItem<'A>` Returns: `OntologyItem<'A> seq`	Splits an OntologyEntry with seperator concatenated TermIds separator : `char` item : `OntologyItem<'A>` Returns: `OntologyItem<'A> seq`