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java.lang.Objectmethods.scores.bootstrap.Bootstrap
public class Bootstrap
Contains methods for the calculation of protein interaction scores using the Bootstrap approach according to
Caroline C. Friedel, Jan Krumsiek, Ralf Zimmer
Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast.
RECOMB 2008, LNBI 4955, pp. 3-16.
This class is not instantiatable.
Method Summary | |
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static ComplexSet |
calculateOptimalSharedProteinsSet(ComplexSet complexes,
ProteinNetwork scores,
float lambda)
Calculates the complex set with added shared proteins using a given scores network. |
static BootstrapMCLClusterings |
clusterForSample(ProteinNetwork scores,
ArrayList<Float> inflationCoefficients)
Performs MCL clustering of a given scores network with a set of inflation coefficient. |
static BootstrapMCLClusterings |
clusterForSample(ProteinNetwork scores,
Float... inflationCoefficients)
Performs MCL clustering of a given scores network with a set of inflation coefficient. |
static ProteinNetwork |
createBootstrapNetwork(Collection<ComplexSet> clusterings)
Creates the bootstrap network for a given set of clusterings. |
static ArrayList<ComplexSet> |
extractClusteringsWithOptimalInflation(ArrayList<BootstrapMCLClusterings> clusteringLists,
float optimalInflation)
Extracts clusterings created with a given inflation coefficient (should be the optimal one) from a set of clusterings. |
static float |
findBestInflation(ArrayList<BootstrapMCLClusterings> clusteringsOnlyEff)
Finds the best inflation coefficient from a given set of clusterings. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public static ArrayList<ComplexSet> extractClusteringsWithOptimalInflation(ArrayList<BootstrapMCLClusterings> clusteringLists, float optimalInflation)
set
- of clusteringsoptimalInflation
- inflation coefficient for which the clusterings
will be extracted
public static ProteinNetwork createBootstrapNetwork(Collection<ComplexSet> clusterings)
clusterings
- set of clusterings for which the boostrap network is calculated
public static BootstrapMCLClusterings clusterForSample(ProteinNetwork scores, Float... inflationCoefficients)
scores
- scores network to be clusteredinflationCoefficients
- inflation coefficients to be used
public static BootstrapMCLClusterings clusterForSample(ProteinNetwork scores, ArrayList<Float> inflationCoefficients)
scores
- scores network to be clusteredinflationCoefficients
- inflation coefficients to be used
public static ComplexSet calculateOptimalSharedProteinsSet(ComplexSet complexes, ProteinNetwork scores, float lambda)
complexes
- complex set for which shared proteins are calculatedscores
- scores network to be used for evaluationlambda
- lambda parameter (see description of this method)
public static float findBestInflation(ArrayList<BootstrapMCLClusterings> clusteringsOnlyEff)
Note: The clustering objects do not have to contain actual clusterings,
inflation coefficient and efficiency are enough. See also:
BootstrapMCLClusterings.BootstrapMCLClusterings(String, boolean)
clusteringsOnlyEff
- clusterings list from which the best inflation
coeffient is determined
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