프로퍼티 | 타입 | 설명 | |
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AnnotationType | AnnotationType | ||
CsvFiles | List |
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DuplexQuantitation | bool | ||
FastaFile | string | ||
FilterQuantInterference | bool | ||
IgnorePeptideWithMissingData | bool | ||
IncludeNonFilteredResults | bool | ||
MaxFdr | double | ||
MaxMissedCleavages | int | ||
MinPeptidesPerGroup | int | ||
MinimumPeptideLength | int | ||
ModificationsToIgnore | HashSet |
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OutputDirectory | string | ||
PScoreCalculationMethod | PScoreCalculateionMethod | ||
ParismonyPeptidesFiltered | List | ||
ParsimonyPeptides | List | ||
Proteases | HashSet |
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ProteinsPerMinute | bool | ||
QuantInterferenceCutoff | double | ||
SemiDigestion | bool | ||
SequenceCoverageMap | bool | ||
UseConservativePScore | bool | ||
UseMedianForQuantitation | bool | ||
UseOnlyCompleteSets | bool | ||
UseQuant | bool |
메소드 | 설명 | |
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Herd ( ) : void |
Main algorithm for mapping peptides to proteins, and grouping proteins into protein groups
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Log ( string message ) : void | ||
ProgressUpdate ( double percent ) : void | ||
ProteinHoarder ( IEnumerable |
메소드 | 설명 | |
---|---|---|
OnUpdateLog ( |
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OnUpdateProgress ( |
메소드 | 설명 | |
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CleanUp ( ) : void |
Free memory of data structures used and tell the main form to reactivate
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ExtraInfo ( List |
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GetAllUniquePeptides ( IEnumerable |
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.
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GetMappedProteinsFromFasta ( string fastaFile, Peptide>.Dictionary |
Performs an in silico digestion of all the proteins found within the fasta file.
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GroupExperiments ( IEnumerable |
Maps the peptide to all the protein groups that it is apart of
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GroupProteins ( 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.
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WriteGroups ( ExperimentGroup>.Dictionary |
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WritePeptides ( ExperimentGroup>.Dictionary |
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WriteProteinsPerMinute ( List |
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WriteSequenceMaps ( List |
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WriteSummary ( ExperimentGroup>.Dictionary |
protected OnUpdateProgress ( |
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e | ||
리턴 | void |
public ProteinHoarder ( IEnumerable |
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csvFiles | IEnumerable |
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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 | |
리턴 | System |
public static bool IgnorePeptideWithMissingData | ||
리턴 | bool |
public static PScoreCalculateionMethod PScoreCalculationMethod | ||
리턴 | PScoreCalculateionMethod |
public static Dictionary |
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리턴 | List |