The NetMan class is a "manager" that controls the behaviour of the active-networks software by reading and storing command-line options and dispatching appropriate actions. More...

#include <netman.h>

Public Member Functions
virtual void	setParameters (int argc, char **argv)
	Set internal parameters based on command line arguments.
void	setComputeBetweennessCentralities ()
bool	getComputeBetweennessCentralities () const
void	setOBOFile (char *file)
void	setClassFile (string name)
string	getClassFile (void) const
void	setCorrelationThreshold (float arg)
bool	getComputeNetworkLegoStability () const
void	setUseRandomisedGEData ()
bool	getUseRandomisedGEData () const
string	getCorrelationMethod () const
MyNT	getCorrelationThreshold () const
void	addDirectory (char *dir)
unsigned int	getNumDirectories () const
string	getDirectory (unsigned int index) const
void	setComputeDenseFunctions ()
bool	getComputeDenseFunctions () const
void	setActiveNetworksEdgesFile (string file)
	Set the name of the file containing the edges in ActiveNetworks.
string	getActiveNetworksEdgesFile () const
	Get the name of the file containing the edges in ActiveNetworks.
bool	getProcessComputedActiveNetworks () const
	Return true if I am processing a previously computed file of active network or network lego nodes or edges.
string	getExperimentName () const
void	setNodeAnnotationsFile (char *name)
void	setGEfile (char *name)
string	getGEfile (void) const
void	addIgnoredEdgeType (string type)
bool	getComputeActiveNetworks (void) const
void	setComputeNetworkLegos ()
bool	getComputeNetworkLegos () const
bool	setFunctionSubgraphsFile (string arg)
void	setMultipleHypothesesCorrectionTest (string optarg)
LIBENRICHMENT_TEST_TYPE	getMultipleHypothesesCorrectionTest () const
void	setMinNumberConditions (unsigned int min)
unsigned int	getMinNumberConditions () const
void	setMinNumberInteractions (unsigned int min)
unsigned int	getMinNumberInteractions () const
void	setNetworkFile (char *file)
string	getNetworkFile (void) const
void	setActiveNetworksNodesFile (string file)
	Set the name of the file containing the nodes in ActiveNetworks.
string	getActiveNetworksNodesFile () const
	Get the name of the file containing the nodes in ActiveNetworks.
bool	getProcessNetwork () const
	Return true if I should simply process an interaction network.
string	getLayoutConstraintsFile () const
void	setPvalueThreshold (float thresh)
MyNT	getPvalueThreshold () const
bool	getComputePathwayPerturbation () const
void	setNumRandomRuns (unsigned int num)
void	setOnlyRandomRuns ()
bool	getOnlyRandomRuns () const
unsigned int	getNumRandomRuns () const
MyNT	getRegulationBound () const
MyNT	getUpRegulationBound () const
MyNT	getDownRegulationBound () const
string	getRegulationMethod () const
unsigned int	getSimulatedAnnealingFactorNumberIterations () const
bool	getSparsifyNetwork () const
string	getSparsificationMethod () const
void	setSplitActiveNetworksIntoComponents ()
bool	getSplitActiveNetworksIntoComponents () const
bool	getSplitGEData () const
void	setEdgeWeightThreshold (string optarg)
void	setEdgeWeightThreshold (MyNT thresh)
MyNT	getEdgeWeightThreshold () const
void	setUseStudentsTDistribution ()
bool	getUseStudentsTDistribution () const
bool	getTranslateAnnotations () const
bool	getComputeTrivialNetworkLegos () const
void	setExpandActiveNetworks ()
bool	getExpandActiveNetworks () const
void	setComputeActiveNetworksTillTheBitterEnd ()
bool	getComputeActiveNetworksTillTheBitterEnd () const
bool	getEmbedActiveNetworkInSuperGraph () const
bool	getCreateWebPages () const
void	createWebPages (SetOfActiveNetworks &anetSet)
	Create web pages describing ActiveNetworks, NetworkLegos, the genes and interactions in them, the functions enriched in them, and containing their layouts.
string	getWWWParametersDir () const
void	getWiringDiagram (MyGraph &wd)
	Return the wiring diagram.
void	getWiringDiagramNodes (set< string > &nodes) const
	Return the set of nodes in the wiring diagram.
string	getEdgeAnnotationsFile (void) const
	Return the name of the file containing annotations for edges/interactions.
void	getNodeAnnotationsFiles (vector< string > &files) const
string	getNodeAnnotationsFile (unsigned int index) const
unsigned int	getNumNodeAnnotationsFiles () const
string	getNodeAliasFile () const
	Return the name of the file containing node aliases.
string	getFunctionSubgraphsFile () const
string	getOBOFile (void) const
string	getTreatmentControlFile () const
	Return the name of the file containing treatment-control pairs.
void	readEdgeAnnotations (string name)
	Read functional annotations for edges/interactions from a file.
void	readNodeAliases (string file)
void	readNodeAnnotations (string name, set< string > *geneSet=NULL)
void	readOBO (string name)
bool	readFunctionSubgraphs (string)
bool	readGEData (string)
bool	readNetwork (string, MyNT minimumEdgeWeight=0)
vector< SetOfPPNodeStats >	treatAliases (MyGraph &pathway, const GEData &geData)
bool	allowNegativeEdgeWeight (set< string > &types) const
void	computeDenseFunctions (ostream *fstr, map< string, MyGraph > &denseFunctionSubgraphs)
void	computeDenseFunctions (ostream *fstr=NULL)
void	computePathwayPerturbation ()
	Compute the perturbation of each pathway in each treatment-control gene expression data set pair.
void	computePathwayPerturbation (const map< string, set< string > > &treatmentControlPairs, map< string, MyGraph > &pathways)
	Compute the perturbation of multiple pathways for a set of contrasts.
void	computePathwayPerturbation (MyGraph &pathway, const GEData &treatment, const GEData &control, string contrast, ActiveNetwork &subgraph)
	Compute the perturbation of pathway in the treatment-control gene expression data set pair.
void	computePathwayPerturbation (MyGraph &pathway, const GEData &geData)
void	plotExpressionValuesHistogram ()
	Plot the histogram of expression values for the current gene expression data set using gnuplot.
void	plotExpressionCorrelationsHistogram ()
	Plot the histogram of correlations between the expression profiles of pairs of genes in the current gene expression set using gnuplot.
void	processNetworkLegos (SetOfActiveNetworks &anetSet)
void	readDirectories ()
void	removeUnresponsiveGenes (GEData &gedata)
	Remove genes from a gene expression data set that have not responsed to the treatment/condition.
bool	computeCorrelations (MyGraph &wiring)
	Compute the weights of the edges in the graph wiring based on the expression values in the current gene expression data set.
bool	computeDenseSubgraphs (vector< ActiveNetwork > &denseSubgraphs, bool randomRun=false)
void	setWiringDiagramEdgeWeightsFS ()
	Reweight edges in wiringDiagram to have FS-Weights.
void	setWiringDiagramEdgeWeightsCD ()
	Reweight edges in wiringDiagram to have CD-distances.
void	postProcess (SetOfActiveNetworks &anetSet)
void	process ()
void	processComputedActiveNetworks ()
void	processFunctionSubgraphs ()
void	processNetwork ()
void	randomise (MyHistogram &histogram)
void	separateDenseFunctions ()
void	_openOutputFiles ()
void	_closeOutputFiles ()
Public Attributes
vector< GEData >	geData
map< string, set< string > >	_nodeAliases
map< string, set< string > >	_reversedNodeAliases
ofstream	binaryMatrixStream
ofstream	conditionStream
ofstream	edgeStream
ofstream	edgeCentralityStream
ofstream	edgeEnrichmentStream
ofstream	edgeEnrichedFunctionStream
ofstream	edgeSimilarityGraphStream
ofstream	edgeTypesCountStream
ofstream	edgeWeightsHistogramStream
ofstream	functionSubgraphsStream
ofstream	expressionValuesHistogramStream
ofstream	histogramStream
ofstream	latticeStream
ofstream	closedLatticeStream
ofstream	logStream
ofstream	nodeStream
ofstream	nodeCentralityStream
ofstream	nodeEnrichmentStream
ofstream	nodeEnrichmentOntologizerStream
ofstream	nodeEnrichedFunctionStream
ofstream	processedNodeEnrichmentsStream
ofstream	processedNodeEnrichmentsOntologizerStream
ofstream	nodeSimilarityGraphStream
ofstream	nodeWeightsHistogramStream
ofstream	itemsetStream
ofstream	randomStream
ofstream	randomPvaluesStream
ofstream	statsStream
stringstream	logStringStream
map< string, string >	_outputFileNames
map< string, ofstream * >	outputStreams

Detailed Description

The NetMan class is a "manager" that controls the behaviour of the active-networks software by reading and storing command-line options and dispatching appropriate actions.

Member Function Documentation

void NetMan::_openOutputFiles ( void )

bool NetMan::allowNegativeEdgeWeight ( set< string > & types ) const [inline]

Check if one of the edge types allows negative correlations.

bool NetMan::computeCorrelations ( MyGraph & wiring )

Compute the weights of the edges in the graph wiring based on the expression values in the current gene expression data set.

Parameters:

inout] wiring, a reference to a MyGraph containing the graph whose edge weights the method computes.

For each edge in wiring, the method computes the absolute value of the correlations of the gene expression profiles of the genes incident on the edge. The correlation is zero if either of the genes is not present in the gene expression data set. The method deletes all edges with weight 0 from wiring and also deletes any resulting nodes that have degree 0.

void NetMan::computeDenseFunctions	(	ostream *	fstr,
		map< string, MyGraph > &	denseFunctionSubgraphs
	)

Find cross-condition and condtion-exclusive ActiveNetworks.

[in] activeNetworkFiles, a vector of files containing ActiveNetworks.

The method reads ActiveNetworks in these files, and constructs the intersection of all possible combinations of ActiveNetworks, using a version of the apriori algorithm that finds maximal itemsets in a binary matrix. The matrix created here is one whose columns are edges and whose rows are ActiveNetworks; an entry is 1 for an edge if it belongs to the ActiveNetwork.

Find functions whose nodes induce dense subgraphs.

Parameters:

[in]	fstr,a	pointer to a file stream. If the pointer is not NULL, the method prints statistics on the subgraph induced by each function to the stream.
[out]	denseFunctionSubgraphs,a	map keyed by function ID. Each value is the corresponding function subgraph.

For each function, the method computes the subgraph of the wiring diagram induced by the genes annotated with that function. If the density of the subgraph is at least 4 (at arbitrary choice) and the completeness is at least 0.5, the method adds that subgraph to denseFunctionSubgraphs.

Warning:: Invoke this method only after invoking NetMan::readAnnotations() and NetMan::readNetwork()!

void NetMan::computeDenseFunctions ( ostream * fstr = NULL ) [inline]

Just like computeDenseFunctions(ofstream, map< string, MyGraph >) except that it stores the dense subgraphs internally.

The method also computes and stores the union of all the dense subgraphs.

void NetMan::computePathwayPerturbation ( )

Compute the perturbation of each pathway in each treatment-control gene expression data set pair.

(i) Read pathway file (one file with all pathways: node1, node2, pathway) and store as a set of graphs.

(ii) Read gene expression file and class file, split if necessary.

(iii) Read treatment-control file (first column contains treatment class, second column contains control class).

(iv) For every t-c pair, invoke the pathway perturbation algorithm. compute z-score of each gene. for every pathway, compute z-score of every edge and then the most activated sub-pathway.

void NetMan::computePathwayPerturbation	(	const map< string, set< string > > &	treatmentControlPairs,
		map< string, MyGraph > &	pathways
	)

Compute the perturbation of multiple pathways for a set of contrasts.

Given multiple pathways, indexed by name, compute the perturbation of each pathway in each of a set of contrasts. Use this method to repeat the analaysis in the paper by Rivera, Tyler, and Murali.

Parameters:

[in]	treatmentControlPairs	a map of sets: the keys of the map are different treatment names and the value for each key is a set of controls. The method will compute a different contrast for each treatment-control pair.
[in]	pathways	a map of instances of MyGraph, keyed by name of the pathway.

void NetMan::computePathwayPerturbation	(	MyGraph &	pathway,
		const GEData &	treatment,
		const GEData &	control,
		string	contrast,
		ActiveNetwork &	subgraph
	)

Compute the perturbation of pathway in the treatment-control gene expression data set pair.

For the input treatment-control pair, compute the z-score of each gene and the z-score of every edge in pathway. Use the edge scores to compute the most perturbed sub-pathway.

Parameters:

[in]	pathway	an instance of MyGraph containing the pathway.
[in]	treatment	an instance of GEData containing the gene expression data for the treatment.
[in]	control	an instance of GEData containing the gene expression data for the control.
[in]	contrast	a string naming the contrast.
[out]	subgraph	an instance of ActiveNetwork containing the most perturbed subgraph.

bool NetMan::getEmbedActiveNetworkInSuperGraph ( ) const [inline]

Return true if the layout of an ActiveNetwork or NetworkLego should display it embedded in the wiring diagram.

bool NetMan::getProcessComputedActiveNetworks ( ) const [inline]

Return true if I am processing a previously computed file of active network or network lego nodes or edges.

Note:: This method is a simple substitute for checking if NetMan::getActiveNetworksEdgesFile() or NetMan::getActiveNetworksNodesFile() returns an empty string or not.

void NetMan::postProcess ( SetOfActiveNetworks & anetSet )

Post-process computed ActiveNetworks in multiple ways.

Parameters:

inout] anetSet, a set of ActiveNetworks.

The method computes the union of the ActiveNetworks in anetSet, the functions enriched in each ActiveNetwork, the betweenness centralities of the nodes and edges in the union, and prints all these statistics to various output files.

void NetMan::process ( void )

The main workhorse of the ActiveNetworks system.

void NetMan::processComputedActiveNetworks ( )

Process already computed ActiveNetworks.

Use this method to post-process ActiveNetworks computed by another programme. A typical use of the method is to process combined ActiveNetworks (for multiple conditions) computed by a programme such as CHARM or Apriori.

void NetMan::processFunctionSubgraphs ( )

The main workhorse of last-resort ActiveNetworks system.

void NetMan::processNetwork ( void )

If there are no gene expression datasets, compute ActiveNetworks in the wiring diagram.

void NetMan::processNetworkLegos ( SetOfActiveNetworks & anetSet )

Computes NetworkLegos by combining the ActiveNetworks in anetSet.

void NetMan::readNodeAliases ( string file )

Read node aliases from file.

Parameters:

[in] file,name of tab-delimited text file containing node aliases. Each line contains a node ID followed by the node alias. Multiple node aliases should appear on separate lines.

void NetMan::readNodeAnnotations	(	string	name,
		set< string > *	geneSet = `NULL`
	)

Read functional annotations for nodes/genes from a file and perform transitive closure, if necessary.

Parameters:

[in]	name,the	name of the file to read annotations from.
[in]	geneSet,a	pointer to a set of genes. If this pointer is not NULL, the method keep annotations only for the genes in the set.

Note:: If you want the method to perform transitive closure for (GO) functional annotations, always invoke this method after Netman::readOBO().

void NetMan::removeUnresponsiveGenes ( GEData & gedata )

Remove genes from a gene expression data set that have not responsed to the treatment/condition.

Parameters:

[in] geData,a reference to an instance of GEData.

The method considers a gene to be unresponsive if all its expression values are between Netman::getDownRegulationBound() and Netman::getUpRegulationBound(). The method "hides" all such genes from further processing.

void NetMan::separateDenseFunctions ( )

Split the wiring diagram into subgraphs: all the dense function subgraphs and the rest.

Member Data Documentation

map< string, set< string > > NetMan::_nodeAliases

ofstream NetMan::binaryMatrixStream

vector< GEData > NetMan::geData

The documentation for this class was generated from the following files:

/home/poirel/src/c++/biorithm/active-networks/netman.h
/home/poirel/src/c++/biorithm/active-networks/netman.C

Public Member Functions

Public Attributes

Detailed Description

Member Function Documentation

Member Data Documentation