PeptideClassification (BioFSharp) | BioFSharp

PeptideClassification Module

Namespace: BioFSharp
Assembly: BioFSharp.dll

Contains functions to classify peptides based on their specificity when mapped to proteins

Types

Type	Description
PeptideEvidenceClass	A marker for unambiguity of a peptide in protein inference
ProteinModel<'id, 'chromosomeId, 'geneLocus, 'sequence>	Contains protein sequence and information about protein used to deduce its relation to other proteins
ProteinModelInfo<'id, 'chromosomeId, 'geneLocus>	Contains information about protein used to deduce its relation to other proteins
StrandDirection	Direction of strand

Functions and values

Function or value	Description
`classify lookUp (peptide, proteinInfos)` Full Usage: `classify lookUp (peptide, proteinInfos)` Parameters: lookUp : `Dictionary<'geneLocus, int>` peptide : `'a` proteinInfos : `ProteinModelInfo<'b, 'c, 'geneLocus> seq` Returns: `PeptideEvidenceClass * 'a`	Assigns a PeptideEvidenceClass to the peptide by using the information given through lookup and proteinInfos lookUp : `Dictionary<'geneLocus, int>` peptide : `'a` proteinInfos : `ProteinModelInfo<'b, 'c, 'geneLocus> seq` Returns: `PeptideEvidenceClass * 'a`
`createLocusSpliceVariantCount ppRelation` Full Usage: `createLocusSpliceVariantCount ppRelation` Parameters: ppRelation : `BidirectionalDictionary<'sequence, ProteinModelInfo<'id, 'chromosomeId, 'geneLocus>>` Returns: `Dictionary<'geneLocus, int>`	ppRelation : `BidirectionalDictionary<'sequence, ProteinModelInfo<'id, 'chromosomeId, 'geneLocus>>` Returns: `Dictionary<'geneLocus, int>`
`createPeptideProteinRelation digest protModels` Full Usage: `createPeptideProteinRelation digest protModels` Parameters: digest : `'sequence -> 'a` protModels : `ProteinModel<'id, 'chromosomeId, 'geneLocus, 'sequence> option seq` Returns: `BidirectionalDictionary<'sequence, ProteinModelInfo<'id, 'chromosomeId, 'geneLocus>>`	Creates a lookup data base to assign peptides to the proteins they are contained in digest : `'sequence -> 'a` protModels : `ProteinModel<'id, 'chromosomeId, 'geneLocus, 'sequence> option seq` Returns: `BidirectionalDictionary<'sequence, ProteinModelInfo<'id, 'chromosomeId, 'geneLocus>>`
`createProteinModel proteinModelInfo sequence` Full Usage: `createProteinModel proteinModelInfo sequence` Parameters: proteinModelInfo : `ProteinModelInfo<'a, 'b, 'c>` sequence : `'d` Returns: `ProteinModel<'a, 'b, 'c, 'd>`	Helper function proteinModelInfo : `ProteinModelInfo<'a, 'b, 'c>` sequence : `'d` Returns: `ProteinModel<'a, 'b, 'c, 'd>`
`createProteinModelInfo id chromosomeId strand geneLocus spliceVariantId seqEquivalents orthologs` Full Usage: `createProteinModelInfo id chromosomeId strand geneLocus spliceVariantId seqEquivalents orthologs` Parameters: id : `'a` chromosomeId : `'b` strand : `StrandDirection` geneLocus : `'c` spliceVariantId : `int` seqEquivalents : `ProteinModelInfo<'a, 'b, 'c> seq` orthologs : `ProteinModelInfo<'a, 'b, 'c> seq` Returns: `ProteinModelInfo<'a, 'b, 'c>`	Helper function to create ProteinModelInfo id : `'a` chromosomeId : `'b` strand : `StrandDirection` geneLocus : `'c` spliceVariantId : `int` seqEquivalents : `ProteinModelInfo<'a, 'b, 'c> seq` orthologs : `ProteinModelInfo<'a, 'b, 'c> seq` Returns: `ProteinModelInfo<'a, 'b, 'c>`