ProteinInference (BioFSharp.Mz)

ProteinInference Module

Namespace: BioFSharp.Mz
Assembly: BioFSharp.Mz.dll

Types and nested modules

Type/Module	Description
MAYU
InferredProteinClassItem<'sequence>	For a group of proteins, contains information about all peptides that might be used for its quantification.
InferredProteinClassItemQValue	For a group of proteins, contains information about all peptides that might be used for its quantification and score / q-value calculated for it.
InferredProteinClassItemScored	For a group of proteins, contains information about all peptides that might be used for its quantification and score calculated for it.
IntegrationStrictness	Used to decide wether overlapping groups of proteins should be kept or merged
PSMInput
PeptideUsageForQuantification	Used to decide which peptides should be used for quantification of protein groups
ProteinClassItem<'sequence>	For a single peptide Sequence, contains information about all proteins it might originate from and its evidence class.
Result	For a group of proteins, contains information about all peptides that are put into the output file.

Functions and values

Function or value	Description
`assignDecoyScoreToTargetScore proteins decoyScores` Full Usage: `assignDecoyScoreToTargetScore proteins decoyScores` Parameters: proteins : `string` decoyScores : `Map<string, (float * string[])>` Returns: `float`	Looks if the given protein accession is present in a map of identified decoy proteins and assigns its score when found. proteins : `string` decoyScores : `Map<string, (float * string[])>` Returns: `float`
`assignPeptideScores peptideSequences peptideScoreMap` Full Usage: `assignPeptideScores peptideSequences peptideScoreMap` Parameters: peptideSequences : `string[]` peptideScoreMap : `Map<string, float>` Returns: `float`	Sums up score of all peptide sequences peptideSequences : `string[]` peptideScoreMap : `Map<string, float>` Returns: `float`
`assignQValueToIPCIS qValueF item` Full Usage: `assignQValueToIPCIS qValueF item` Parameters: qValueF : `float -> float` item : `InferredProteinClassItemScored` Returns: `InferredProteinClassItemQValue`	qValueF : `float -> float` item : `InferredProteinClassItemScored` Returns: `InferredProteinClassItemQValue`
`assignTranscriptsToGenes tryParseProteinID gffLines` Full Usage: `assignTranscriptsToGenes tryParseProteinID gffLines` Parameters: tryParseProteinID : `string -> 'a option` gffLines : `GFFLine<'a0> seq` Returns: `Map<'a, ProteinModelInfo<string, string, string>>`	By reading GFF creates the protein models (relationships of proteins to each other) which basically means grouping the rnas over the gene loci TODO: Don't group over order but rather group over id tryParseProteinID : `string -> 'a option` gffLines : `GFFLine<'a0> seq` Returns: `Map<'a, ProteinModelInfo<string, string, string>>`
`calculateFDRwithDecoyTargetRatio data` Full Usage: `calculateFDRwithDecoyTargetRatio data` Parameters: data : `InferredProteinClassItemScored[]` Returns: `float`	Calculates Decoy/Target ratio data : `InferredProteinClassItemScored[]` Returns: `float`
`calculateFDRwithMAYU data proteinsFromDB` Full Usage: `calculateFDRwithMAYU data proteinsFromDB` Parameters: data : `InferredProteinClassItemScored[]` proteinsFromDB : `(string * string)[]` Returns: `float`	Calculates the fdr of the data using the MAYU method. The proteinsFromDB is the DB that was used for the inference. data : `InferredProteinClassItemScored[]` proteinsFromDB : `(string * string)[]` Returns: `float`
`createInferredProteinClassItemOut proteinIDs evidenceClass peptideSequences targetScore decoyScore qValue` Full Usage: `createInferredProteinClassItemOut proteinIDs evidenceClass peptideSequences targetScore decoyScore qValue` Parameters: proteinIDs : `string` evidenceClass : `PeptideEvidenceClass` peptideSequences : `string` targetScore : `float` decoyScore : `float` qValue : `float` Returns: `Result`	proteinIDs : `string` evidenceClass : `PeptideEvidenceClass` peptideSequences : `string` targetScore : `float` decoyScore : `float` qValue : `float` Returns: `Result`
`createInferredProteinClassItemQValue infProtClassItemScored qValue` Full Usage: `createInferredProteinClassItemQValue infProtClassItemScored qValue` Parameters: infProtClassItemScored : `InferredProteinClassItemScored` qValue : `float` Returns: `InferredProteinClassItemQValue`	infProtClassItemScored : `InferredProteinClassItemScored` qValue : `float` Returns: `InferredProteinClassItemQValue`
`createInferredProteinClassItemScored proteinIDs evidenceClass peptideSequences targetScore decoyScore isDecoy decoyHasBetterScore foundInDB` Full Usage: `createInferredProteinClassItemScored proteinIDs evidenceClass peptideSequences targetScore decoyScore isDecoy decoyHasBetterScore foundInDB` Parameters: proteinIDs : `string` evidenceClass : `PeptideEvidenceClass` peptideSequences : `string[]` targetScore : `float` decoyScore : `float` isDecoy : `bool` decoyHasBetterScore : `bool` foundInDB : `bool` Returns: `InferredProteinClassItemScored`	proteinIDs : `string` evidenceClass : `PeptideEvidenceClass` peptideSequences : `string[]` targetScore : `float` decoyScore : `float` isDecoy : `bool` decoyHasBetterScore : `bool` foundInDB : `bool` Returns: `InferredProteinClassItemScored`
`createPeptideProteinRelation protModels` Full Usage: `createPeptideProteinRelation protModels` Parameters: protModels : `ProteinModel<'id, 'chromosomeId, 'geneLocus, 'sequence list> option seq` Returns: `BidirectionalDictionary<'sequence, ProteinModelInfo<'id, 'chromosomeId, 'geneLocus>>`	Creates a lookup data base to assign peptides to the proteins they are contained in protModels : `ProteinModel<'id, 'chromosomeId, 'geneLocus, 'sequence list> option seq` Returns: `BidirectionalDictionary<'sequence, ProteinModelInfo<'id, 'chromosomeId, 'geneLocus>>`
`createPeptideScoreMap psmInputs` Full Usage: `createPeptideScoreMap psmInputs` Parameters: psmInputs : `PSMInput list list` Returns: `Map<string, float>`	psmInputs : `PSMInput list list` Returns: `Map<string, float>`
`createProteinClassItem proteinIDs evidenceClass peptideSequence` Full Usage: `createProteinClassItem proteinIDs evidenceClass peptideSequence` Parameters: proteinIDs : `string[]` evidenceClass : `PeptideEvidenceClass` peptideSequence : `'sequence` Returns: `ProteinClassItem<'sequence>`	proteinIDs : `string[]` evidenceClass : `PeptideEvidenceClass` peptideSequence : `'sequence` Returns: `ProteinClassItem<'sequence>`
`createProteinModelInfoFromEntry i locus entry` Full Usage: `createProteinModelInfoFromEntry i locus entry` Parameters: i : `int` locus : `string` entry : `GFFEntry` Returns: `ProteinModelInfo<string, string, string>`	Reads geographical information about protein from gff entry and builds the modelinfo of it This function takes an RNA gff3 entry and therefore will contain the splice variant id of the gene in its result. This splice variant id should be the same in the given FastA-file. i : `int` locus : `string` entry : `GFFEntry` Returns: `ProteinModelInfo<string, string, string>`
`createProteinToPepSequencesMap proteinClassItems` Full Usage: `createProteinToPepSequencesMap proteinClassItems` Parameters: proteinClassItems : `ProteinClassItem<'sequence> list` Returns: `Map<string, ProteinClassItem<'sequence> list>`	Used to map the resulting protein groups to the sequences which are used for their quantification proteinClassItems : `ProteinClassItem<'sequence> list` Returns: `Map<string, ProteinClassItem<'sequence> list>`
`createReverseProteinScores reverseProteins peptideScoreMap` Full Usage: `createReverseProteinScores reverseProteins peptideScoreMap` Parameters: reverseProteins : `(string * string[])[]` peptideScoreMap : `Map<string, float>` Returns: `Map<string, (float * string[])>`	reverseProteins : `(string * string[])[]` peptideScoreMap : `Map<string, float>` Returns: `Map<string, (float * string[])>`
`inferSequences integrationStrictness peptideUsageForQuantification proteinClassItems` Full Usage: `inferSequences integrationStrictness peptideUsageForQuantification proteinClassItems` Parameters: integrationStrictness : `IntegrationStrictness` peptideUsageForQuantification : `PeptideUsageForQuantification` proteinClassItems : `ProteinClassItem<'sequence> list` Returns: `InferredProteinClassItem<'sequence> seq`	integrationStrictness : `IntegrationStrictness` peptideUsageForQuantification : `PeptideUsageForQuantification` proteinClassItems : `ProteinClassItem<'sequence> list` Returns: `InferredProteinClassItem<'sequence> seq`
`isGene item` Full Usage: `isGene item` Parameters: item : `GFFLine<'a>` Returns: `bool`	Checks if GFF line describes gene item : `GFFLine<'a>` Returns: `bool`
`isRNA item` Full Usage: `isRNA item` Parameters: item : `GFFLine<'a>` Returns: `GFFEntry option`	Checks if GFF line describes rna item : `GFFLine<'a>` Returns: `GFFEntry option`
`proteinGroupToString proteinGroup` Full Usage: `proteinGroupToString proteinGroup` Parameters: proteinGroup : `string[]` Returns: `string`	Appends a collection of proteins to a single string proteinGroup : `string[]` Returns: `string`
`removeModification pepSeq` Full Usage: `removeModification pepSeq` Parameters: pepSeq : `string` Returns: `string`	pepSeq : `string` Returns: `string`