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

Herd() public method

Main algorithm for mapping peptides to proteins, and grouping proteins into protein groups
public Herd ( ) : void
return void

Log() public method

public Log ( string message ) : void
message string
return void

OnUpdateLog() protected method

protected OnUpdateLog ( StatusEventArgs e ) : void
e StatusEventArgs
return void

OnUpdateProgress() protected method

protected OnUpdateProgress ( ProgressEventArgs e ) : void
e ProgressEventArgs
return void

ProgressUpdate() public method

public ProgressUpdate ( double percent ) : void
percent double
return void

ProteinHoarder() public method

public 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
csvFiles IEnumerable
fastaFile string
outputDirectory string
minPeptidesPerGroup int
maxMissedCleavages int
maxFDR double
annotationType AnnotationType
useConservativePScore bool
useQuant bool
useMedian bool
duplexQuantitation bool
useNoiseBandCap bool
modstoignore HashSet
filterquantInterference bool
quantInterferenceCutoff double
includeUnfilteredResults bool
ignorePeptideWithMissingData bool
semiDigestion bool
proteinPerMinute bool
sequenceCoverageMap bool
return System

Property Details

AnnotationType public static property

public static AnnotationType AnnotationType
return AnnotationType

CsvFiles public property

public List CsvFiles
return List

DuplexQuantitation public static property

public static bool DuplexQuantitation
return bool

FastaFile public property

public string FastaFile
return string

FilterQuantInterference public static property

public static bool FilterQuantInterference
return bool

IgnorePeptideWithMissingData public static property

public static bool IgnorePeptideWithMissingData
return bool

IncludeNonFilteredResults public static property

public static bool IncludeNonFilteredResults
return bool

MaxFdr public property

public double MaxFdr
return double

MaxMissedCleavages public property

public int MaxMissedCleavages
return int

MinPeptidesPerGroup public property

public int MinPeptidesPerGroup
return int

MinimumPeptideLength public property

public int MinimumPeptideLength
return int

ModificationsToIgnore public property

public HashSet ModificationsToIgnore
return HashSet

OutputDirectory public property

public string OutputDirectory
return string

PScoreCalculationMethod public static property

public static PScoreCalculateionMethod PScoreCalculationMethod
return PScoreCalculateionMethod

ParismonyPeptidesFiltered public static property

public static Dictionary> ParismonyPeptidesFiltered
return List>.Dictionary

ParsimonyPeptides public static property

public static Dictionary> ParsimonyPeptides
return List>.Dictionary

Proteases public property

public HashSet Proteases
return HashSet

ProteinsPerMinute public static property

public static bool ProteinsPerMinute
return bool

QuantInterferenceCutoff public static property

public static double QuantInterferenceCutoff
return double

SemiDigestion public static property

public static bool SemiDigestion
return bool

SequenceCoverageMap public static property

public static bool SequenceCoverageMap
return bool

UseConservativePScore public static property

public static bool UseConservativePScore
return bool

UseMedianForQuantitation public static property

public static bool UseMedianForQuantitation
return bool

UseOnlyCompleteSets public static property

public static bool UseOnlyCompleteSets
return bool

UseQuant public static property

public static bool UseQuant
return bool