Свойство | Тип | Описание | |
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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 |
||
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 |
Метод | Описание | |
---|---|---|
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 |
Метод | Описание | |
---|---|---|
OnUpdateLog ( |
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OnUpdateProgress ( |
Метод | Описание | |
---|---|---|
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 OnUpdateLog ( |
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e | ||
Результат | void |
protected OnUpdateProgress ( |
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e | ||
Результат | void |
public ProgressUpdate ( double percent ) : void | ||
percent | double | |
Результат | void |
public ProteinHoarder ( IEnumerable |
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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 | |
Результат | System |
public static AnnotationType AnnotationType | ||
Результат | AnnotationType |
public static bool DuplexQuantitation | ||
Результат | bool |
public static bool FilterQuantInterference | ||
Результат | bool |
public static bool IgnorePeptideWithMissingData | ||
Результат | bool |
public static bool IncludeNonFilteredResults | ||
Результат | bool |
public static PScoreCalculateionMethod PScoreCalculationMethod | ||
Результат | PScoreCalculateionMethod |
public static Dictionary |
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Результат | List |
public static Dictionary |
||
Результат | List |
public static bool ProteinsPerMinute | ||
Результат | bool |
public static double QuantInterferenceCutoff | ||
Результат | double |
public static bool SequenceCoverageMap | ||
Результат | bool |
public static bool UseConservativePScore | ||
Результат | bool |
public static bool UseMedianForQuantitation | ||
Результат | bool |
public static bool UseOnlyCompleteSets | ||
Результат | bool |