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• ProteinHoarder

C# Class Coon.Compass.ProteinHoarder.ProteinHoarder

Show file Open project: dbaileychess/Compass Class Usage Examples

Public Properties

Property	Type	Description
AnnotationType	AnnotationType
CsvFiles	List
DuplexQuantitation	bool
FastaFile	string
FilterQuantInterference	bool
IgnorePeptideWithMissingData	bool
IncludeNonFilteredResults	bool
MaxFdr	double
MaxMissedCleavages	int
MinPeptidesPerGroup	int
MinimumPeptideLength	int
ModificationsToIgnore	HashSet
OutputDirectory	string
PScoreCalculationMethod	PScoreCalculateionMethod
ParismonyPeptidesFiltered	List>.Dictionary
ParsimonyPeptides	List>.Dictionary
Proteases	HashSet
ProteinsPerMinute	bool
QuantInterferenceCutoff	double
SemiDigestion	bool
SequenceCoverageMap	bool
UseConservativePScore	bool
UseMedianForQuantitation	bool
UseOnlyCompleteSets	bool
UseQuant	bool

Public Methods

Method	Description
Herd ( ) : void	Main algorithm for mapping peptides to proteins, and grouping proteins into protein groups
Log ( string message ) : void
ProgressUpdate ( double percent ) : void
ProteinHoarder ( IEnumerable csvFiles, string fastaFile, string outputDirectory, int minPeptidesPerGroup = 1, int maxMissedCleavages = 3, double maxFDR = 1, AnnotationType annotationType = AnnotationType.None, bool useConservativePScore = true, bool useQuant = false, bool useMedian = false, bool duplexQuantitation = false, bool useNoiseBandCap = false, HashSet modstoignore = null, bool filterquantInterference = true, double quantInterferenceCutoff = 0.25, bool includeUnfilteredResults = false, bool ignorePeptideWithMissingData = false, bool semiDigestion = false, bool proteinPerMinute = false, bool sequenceCoverageMap = false ) : System

Protected Methods

Method	Description
OnUpdateLog ( StatusEventArgs e ) : void
OnUpdateProgress ( ProgressEventArgs e ) : void

Private Methods

Method	Description
CleanUp ( ) : void	Free memory of data structures used and tell the main form to reactivate
ExtraInfo ( List proteinGroups, string outputDirectory ) : void
GetAllUniquePeptides ( IEnumerable csvFiles ) : Peptide>.Dictionary	Loads all the unique peptide sequences (L / I ambiguous) from the OMSSA csv files supplied. Keeps track of all the psms for those peptides as well.
GetMappedProteinsFromFasta ( string fastaFile, Peptide>.Dictionary uniquePeptides, IList proteases, bool semiDigestion = false ) : List	Performs an in silico digestion of all the proteins found within the fasta file.
GroupExperiments ( IEnumerable csvFiles, bool useQuant ) : ExperimentGroup>.Dictionary	Maps the peptide to all the protein groups that it is apart of
GroupProteins ( List proteins, bool printMessages = true ) : List	Groups proteins into groups based on the peptides in the proteins. Combines Proteins if they contain all the same peptide sequences (Indistinquishable) and removes groups that can be made up by other groups in its entirety (Subsumable). Lastly, it filters for false discovery.
WriteGroups ( ExperimentGroup>.Dictionary expgroups, string outputDirectory ) : void
WritePeptides ( ExperimentGroup>.Dictionary expgroups, string outputDirectory ) : void
WriteProteinsPerMinute ( List allPeptides, List proteins, string outputDirectory ) : void
WriteSequenceMaps ( List proteinGroups, string outputDirectory ) : void
WriteSummary ( ExperimentGroup>.Dictionary expgroups, string outputDirectory ) : void

Method Details

Property Details