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Uses of ComplexSet in procope.data.complexes |
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Methods in procope.data.complexes that return ComplexSet | |
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ComplexSet |
ComplexSet.calculateSharedProteinsBootstrap(ProteinNetwork scores,
float lambda)
Calculates the complex set with added shared proteins using a given scores network. |
ComplexSet |
ComplexSet.calculateSharedProteinsPu(ProteinNetwork interactions,
float a,
float b)
Calculates shared proteins with respect to a given interaction network as proposed by Pu et al., 2007 (Pubmed: 17370254). |
ComplexSet |
ComplexSet.copy()
Creates a copy of this complex set |
ComplexSet |
ComplexSet.decompose(ProteinNetwork scores,
float cutoff)
Decomposes a complex set with respect to a given scores network. |
ComplexSet |
ComplexSet.randomizeByExchanging()
Returns a randomized copy of the complex set. |
ComplexSet |
ComplexSet.randomizeByRemapping()
Returns a randomized copy of the complex set. |
static ComplexSet |
ComplexSetReader.readComplexes(File file)
Reads complexes from a given file. |
static ComplexSet |
ComplexSetReader.readComplexes(File file,
String separator)
Reads complexes from a given file. |
static ComplexSet |
ComplexSetReader.readComplexes(InputStream input)
Reads complexes from a given InputStream. |
static ComplexSet |
ComplexSetReader.readComplexes(InputStream input,
String separator)
Reads complexes from a given InputStream. |
static ComplexSet |
ComplexSetReader.readComplexes(String file)
Reads complexes from a given file. |
static ComplexSet |
ComplexSetReader.readComplexes(String file,
String separator)
Reads complexes from a given file. |
ComplexSet |
ComplexSet.removeComplexesByScore(ProteinNetwork scores,
float cutoff)
Removes all complexes from the complex set whose average edge score between all proteins of the complex regarding a given scores network is below the cutoff. |
ComplexSet |
ComplexSet.removeComplexesByScore(ProteinNetwork scores,
float cutoff,
boolean ignoreMissing)
Removes all complexes from the complex set whose average edge score between all proteins of the complex regarding a given scores network is below the cutoff. |
ComplexSet |
ComplexSet.removeComplexesBySize(int cutoffSize,
boolean below)
Removes all complexes smaller or larger than a given threshold from the complex set. |
ComplexSet |
ComplexSet.removeSingletons()
Removes singletons from the complex set. |
ComplexSet |
ComplexSet.restrictToProteins(Set<Integer> proteins,
boolean fullCoverage)
Returns a new complex set containing only those complexes whose proteins are completely or partially contained in a given set of proteins. |
ComplexSet |
ComplexSet.restrictToProteinSpace(ProteinSet proteins,
boolean fullCoverage)
Returns a new complex set containing only those complexes whose proteins are completely or partially contained in a given set of proteins. |
Methods in procope.data.complexes with parameters of type ComplexSet | |
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static void |
ComplexSetWriter.writeComplexes(ComplexSet set,
File outfile)
Writes a complex set to a specified file. |
static void |
ComplexSetWriter.writeComplexes(ComplexSet set,
File outfile,
String delimiter)
Writes a complex set to a specified file. |
static void |
ComplexSetWriter.writeComplexes(ComplexSet set,
OutputStream outstream)
Writes a complex set to an OutputStream. |
static void |
ComplexSetWriter.writeComplexes(ComplexSet set,
OutputStream outstream,
String delimiter)
Writes a complex set to an OutputStream. |
static void |
ComplexSetWriter.writeComplexes(ComplexSet set,
String outfile)
Writes a complex set to a specified file. |
static void |
ComplexSetWriter.writeComplexes(ComplexSet set,
String outfile,
String delimiter)
Writes a complex set to a specified file. |
static void |
ComplexSetWriter.writeXGMML(ComplexSet set,
ProteinNetwork net,
File outfile)
Creates a Cytoscape-compatible XGMML file. |
static void |
ComplexSetWriter.writeXGMML(ComplexSet set,
ProteinNetwork net,
OutputStream outstream)
Creates a Cytoscape-compatible XGMML file, but writes to an output stream. |
static void |
ComplexSetWriter.writeXGMML(ComplexSet set,
ProteinNetwork net,
String outfile)
Creates a Cytoscape-compatible XGMML file. |
Uses of ComplexSet in procope.data.petrinets |
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Methods in procope.data.petrinets with parameters of type ComplexSet | |
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void |
PetriNetCreator.addComplexSet(ComplexSet set,
String name)
Adds a ComplexSet which will be integrated into the Petri net. |
Uses of ComplexSet in procope.evaluation.comparison |
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Methods in procope.evaluation.comparison that return ComplexSet | |
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ComplexSet |
ComplexMappings.getSetA()
Returns the first complex set involved in this mapping set. |
ComplexSet |
ComplexMappings.getSetB()
Returns the second complex set involved in this mapping set. |
Methods in procope.evaluation.comparison with parameters of type ComplexSet | |
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static BroheeSimilarity |
ComplexSetComparison.broheeComparison(ComplexSet candidate,
ComplexSet reference)
Calculate complex set similarity after |
static int[][] |
ComplexSetComparison.complexSetsOverlap(ComplexSet setA,
ComplexSet setB)
Calculates the overlap matrix for two given complex sets. |
static ComplexMappings |
ComplexSetComparison.mapComplexes(ComplexSet setA,
ComplexSet setB,
int overlapThreshold)
Calculates a mapping between two given complex sets by comparing the protein overlaps of their complexes. |
static ComplexMappings |
ComplexSetComparison.mapComplexesConsistently(ComplexSet setA,
ComplexSet setB,
int overlapThreshold)
Calculates a mapping between two given complex sets by comparing the protein overlaps of their complexes. |
static ComplexMappings |
ComplexSetComparison.mapComplexesExactly(ComplexSet setA,
ComplexSet setB)
Find complexes in two given complex sets which are identical |
static ComplexMappings |
ComplexSetComparison.mapComplexesMultiple(ComplexSet setA,
ComplexSet setB,
int overlapThreshold)
Calculates a mapping between two given complex sets by comparing the protein overlaps of their complexes. |
Constructors in procope.evaluation.comparison with parameters of type ComplexSet | |
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ComplexMappings(ComplexSet setA,
ComplexSet setB,
List<ComplexMapping> mappings)
Creates a new set of complex mappings. |
Uses of ComplexSet in procope.evaluation.complexquality |
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Methods in procope.evaluation.complexquality with parameters of type ComplexSet | |
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float |
Colocalization.getAverageColocalizationScore(ComplexSet complexes,
boolean weighted,
boolean ignoreMissing)
Calculates the average colocalization score for a given complex set. |
float |
Colocalization.getAveragePPV(ComplexSet complexes,
boolean weighted,
boolean ignoreMissing)
Calculates the average PPV for a given complex set. |
Uses of ComplexSet in procope.evaluation.networkperformance |
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Methods in procope.evaluation.networkperformance with parameters of type ComplexSet | |
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static float |
ComplexEnrichment.calculateComplexEnrichment(ProteinNetwork network,
ComplexSet reference,
int numrand,
boolean useWeightedScores)
Calculates the complex enrichment of a given network with respect to a given complex set. |
static List<ROCCurve> |
ROC.calculateROCCurves(List<ProteinNetwork> scoreNetworks,
ComplexSet reference,
ComplexSet referenceForNegativeSet,
LocalizationData locData,
boolean restrictToNetworkProteins)
Calculate the ROC curves for a given set of networks. |
Uses of ComplexSet in procope.examples |
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Methods in procope.examples that return ComplexSet | |
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ComplexSet |
DummyClusterer.cluster(ProteinNetwork net)
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Uses of ComplexSet in procope.methods.clustering |
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Methods in procope.methods.clustering that return ComplexSet | |
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ComplexSet |
MarkovClusterer.cluster(ProteinNetwork net)
Perform MCL clustering. |
ComplexSet |
Clusterer.cluster(ProteinNetwork net)
Calculates a clustering represented as ComplexSet from a given
scores network. |
ComplexSet |
HierarchicalClusterer.cluster(ProteinNetwork net)
Performs hierarchical agglomerative clustering on given similarity network. |
ComplexSet |
HierarchicalTreeNode.extractClustering(float threshold)
Extracts a clustering from this tree by cutting it a given similarity threshold value. |
Methods in procope.methods.clustering with parameters of type ComplexSet | |
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static double |
MCLEfficiencyCalculator.calculateEfficiency(ProteinNetwork network,
ComplexSet clustering)
Calculate performance of the clustering using a given complex network. |
Uses of ComplexSet in procope.methods.scores |
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Methods in procope.methods.scores with parameters of type ComplexSet | |
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static float |
ComplexScoreCalculator.averageComplexSetScore(ProteinNetwork scoreNetwork,
ComplexSet complexSet,
boolean weighted)
Calculates the average complex score of a given complex set. |
static float |
ComplexScoreCalculator.averageComplexSetScore(ProteinNetwork scoreNetwork,
ComplexSet complexSet,
boolean weighted,
boolean ignoreMissingScores)
Calculates the average complex score of a given complex set. |
static float |
ComplexScoreCalculator.averageComplexSetScore(ScoresCalculator scoreCalc,
ComplexSet complexSet,
boolean weighted)
Calculates the average complex score of a given complex set. |
static float |
ComplexScoreCalculator.averageComplexSetScore(ScoresCalculator scoreCalc,
ComplexSet complexSet,
boolean weighted,
boolean ignoreMissingScores)
Calculates the average complex score of a given complex set. |
Uses of ComplexSet in procope.methods.scores.bootstrap |
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Methods in procope.methods.scores.bootstrap that return ComplexSet | |
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ComplexSet |
BootstrapClustering.getClustering()
Returns the clustering. |
Methods in procope.methods.scores.bootstrap that return types with arguments of type ComplexSet | |
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static ArrayList<ComplexSet> |
Bootstrap.extractOptimalClusterings(ArrayList<BootstrapClusterings> clusteringLists,
int optimalIndex)
Extracts all clusterings at a given index of the clustering lists. |
Method parameters in procope.methods.scores.bootstrap with type arguments of type ComplexSet | |
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static ProteinNetwork |
Bootstrap.createBootstrapNetwork(Collection<ComplexSet> clusterings)
Creates the bootstrap network for a given set of clusterings. |
Constructors in procope.methods.scores.bootstrap with parameters of type ComplexSet | |
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BootstrapClustering(ComplexSet set,
String parameters,
float efficiency)
Create new bootstrap MCL clustering result. |
Uses of ComplexSet in procope.tools.userclasses |
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Methods in procope.tools.userclasses that return ComplexSet | |
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ComplexSet |
DummyClusterer.cluster(ProteinNetwork net)
Implementation of the Clusterer.cluster(ProteinNetwork)
method. |
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