The SetOfActiveNetworks class stores a set of ActiveNetworks, all of which share some property. More...

#include <active-networks.h>

Inheritance diagram for SetOfActiveNetworks:

Public Member Functions
void	add (ActiveNetwork &anet)
void	add (vector< ActiveNetwork > &nets)
void	add (Itemset &itemset, unsigned int index)
void	add (vector< Itemset > &itemsets)
void	addCondition (string condition)
virtual void	compareNetworkLegosToActiveNetworks ()
void	computeBinaryMatrix (vector< vector< unsigned int > > &binaryMatrix, map< unsigned int, string > &rowNames, map< unsigned int, string > &columnNames, bool addComplements=false, set< unsigned int > *complementRows=NULL)
	Compute a binary matrix representing memberships of interactions in ActiveNetworks.
void	computeEdgeBetweenessCentrality ()
void	clearEdgeEnrichments ()
	Erase all computed information about edge enrichments in each active network. This method is useful when I want to try different enrichment algorithms in the same run.
void	computeEdgeEnrichments (const MyAnnotations &annotations)
void	computeEdgeSimilarityGraph (MyGraph &graph) const
void	clearNodeEnrichments ()
	Erase all computed information about node enrichments in each active network. This method is useful when I want to try different enrichment algorithms in the same run.
void	computeNodeWeights (const GEData &gedata)
MyNT	computeMostSimilarEdges (const MyGraph &other, unsigned int &bestIndex) const
MyNT	computeMostSimilarNodes (const MyGraph &other, unsigned int &bestIndex) const
void	computeNodeBetweenessCentrality ()
void	computeNodeCounts ()
void	computeNodeSimilarityGraph (MyGraph &graph) const
void	computePvalues (const MyHistogram &histogram)
void	computeSNetwork ()
	Compute the "s"Network formed by the ActiveNetworks.
void	computeUnion (string name, ActiveNetwork &unionActiveNetwork)
void	computeUnion (string name)
void	expand (const GEData &expression, string id, MyNT correlationThreshold)
vector< ActiveNetwork >	getActiveNetworks ()
void	getUnion (ActiveNetwork &unionActiveNetwork)
unsigned int	getNumActiveNetworks () const
	Return the number of ActiveNetworks stored.
void	printConditions (ostream &conditionStream)
void	printEdges (ostream &edgeStream)
void	printEdgeBetweenessCentrality (ostream &edgeCentralityStream)
void	printEdgesItemset (ostream &itemsetStream, string id)
void	printEdgeTypeCounts (ostream &edgeTypesCountStream)
void	printEdgeEnrichments (ostream &edgeEnrichmentStream, ostream &edgeEnrichedFunctionStream)
void	printEdgeWeightsHistograms (ostream &edgeWeightsHistogramStream, string fileName)
void	printNodeEnrichments (ostream &nodeEnrichmentStream, ostream &nodeEnrichedFunctionStream, GeneOntology *go)
	Print tabular information on enriched functions annotating nodes in the active networks.
void	processNodeEnrichments (ostream &processNodeEnrichmentsStream, const GeneOntology *go)
	Analyse patterns in the enriched functions annotating nodes in the active networks.
void	printNodes (ostream &nodeStream)
void	printNodeBetweenessCentrality (ostream &nodeCentralityStream)
void	printNodeWeightsHistograms (ostream &nodeWeightsHistogramStream, string fileName)
void	printStatistics (ostream &statStream)
void	read (const vector< string > &activeNetworkFiles)
void	read (string activeNetworkFile)
void	readEdges (string edgesFile)
virtual void	readMappingFromNetworkLegosToActiveNetworks (string nlsToRNsFile)
	This function is defined in SetOfActiveNetworks only because of an implementation detail in NetMan::processComputedActiveNetworks(). Ideally, this method should be defined only in SetOfNetworkLegos.
void	readNodeEnrichedFunctions (string nodeEnrichedFunctionsFile)
void	readNodeEnrichments (string nodeEnrichmentsFile)
void	readNodes (string nodesFile, MyGraph &superGraph)
Protected Attributes
vector< ActiveNetwork >	_anets
map< string, unsigned int >	_anetIdToIndex
ActiveNetwork	_combinedAnet
map< MyEdge, MyNT >	_edgeCentralities
map< MyNodeId, MyNT >	_nodeCentralities
map< MyNodeId, vector< MyGraph * > >	_nodeCounts
Friends
class	SetOfNetworkLegos

Detailed Description

The SetOfActiveNetworks class stores a set of ActiveNetworks, all of which share some property.

Member Function Documentation

void SetOfActiveNetworks::add ( ActiveNetwork & anet ) [inline]

Add an ActiveNetwork.

void SetOfActiveNetworks::add ( vector< ActiveNetwork > & nets ) [inline]

Add multiple ActiveNetworks.

void SetOfActiveNetworks::add	(	Itemset &	itemset,
		unsigned int	index
	)		`[inline]`

Add an ActiveNetwork stored as an Itemset.

Parameters:

[in]	itemset,a	reference to the Itemset to be added.
[in]	index,the	index of the ActiveNetwork, set/incremented by the caller.

void SetOfActiveNetworks::add ( vector< Itemset > & itemsets ) [inline]

Add multiple ActiveNetworks stored as Itemsets.

void SetOfActiveNetworks::addCondition ( string condition ) [inline]

Add condition to all the ActiveNetworks.

virtual void SetOfActiveNetworks::compareNetworkLegosToActiveNetworks ( ) [inline, virtual]

This function is defined in SetOfActiveNetworks only because of an implementation detail in NetMan::processComputedActiveNetworks(). Ideally, this method should be defined only in SetOfNetworkLegos.

Reimplemented in SetOfNetworkLegos.

void SetOfActiveNetworks::computeBinaryMatrix	(	vector< vector< unsigned int > > &	binaryMatrix,
		map< unsigned int, string > &	rowNames,
		map< unsigned int, string > &	columnNames,
		bool	addComplements = `false`,
		set< unsigned int > *	complementRows = `NULL`
	)

Compute a binary matrix representing memberships of interactions in ActiveNetworks.

Parameters:

[out]	binaryMatrix,a	two-dimensional vector of unsigned ints. Each row represents an ActiveNetwork and each column represents an interaction in an ActiveNetwork.
[out]	rowNames,a	map from the name of an ActiveNetwork to the row it corresponds to in binaryMatrix.
[out]	columnNames,a	map from a string representing an interaction to the column it corresponds to in binaryMatrix.
[in]	addComplements,a	boolean. If this variable is true, the method adds the complement of each ActiveNetwork's binary vector to binaryMatrix. The name of the corresponding row is the name of the ActiveNetwork prefixed by "complement-".
[out]	complementRows,a	pointer to a set of unsigned ints. If addComplements is true and this variable is not NULL, the method adds the indices of the rows corresponding to the ActiveNetwork complements to this set.

Warning:: Invoke this method only after invoking SetOfActiveNetworks::computeUnion().

Note:: The running time of this method is $O(mn + m m)$, where $m$ is the total number of interactions in all the ActiveNetworks and $n$ is the number of ActiveNetworks.

void SetOfActiveNetworks::computeEdgeBetweenessCentrality ( )

For each interaction (edge) in the union of all ActiveNetworks, compute its betweenness centrality and store them internally.

void SetOfActiveNetworks::computeEdgeEnrichments ( const MyAnnotations & annotations )

Compute the functions enriched in the edges of each ActiveNetwork.

Parameters:

[in] annotations,functional annotations for all the edges in the ActiveNetwork.

The method uses the set of all edges with functional annotations in the argument as the universal set.

void SetOfActiveNetworks::computeEdgeSimilarityGraph ( MyGraph & graph ) const

Compute a graph representing the similarity of the edge sets of the ActiveNetworks.

The method constructs a graph where each node is an active network and the weight of each edge is the set similarity of the edge sets of the two active networks connected by the edge.

MyNT SetOfActiveNetworks::computeMostSimilarEdges	(	const MyGraph &	other,
		unsigned int &	bestIndex
	)		const

Compute the ActiveNetwork most similar to other based on common edges.

Parameters:

[in]	other,an	instance of MyGraph.
[out]	bestIndex,the	index in the invocant of the most similar ActiveNetwork.

Returns:: the value of the similarity.

MyNT SetOfActiveNetworks::computeMostSimilarNodes	(	const MyGraph &	other,
		unsigned int &	bestIndex
	)		const

Compute the ActiveNetwork most similar to other based on common nodes.

Parameters:

[in]	other,an	instance of MyGraph.
[out]	bestIndex,the	index in the invocant of the most similar ActiveNetwork.

Returns:: the value of the similarity.

void SetOfActiveNetworks::computeNodeBetweenessCentrality ( )

Compute NetworkLegos based on the ActiveNetworks in the invocant. For each node in the union of all ActiveNetworks, compute its betweenness centrality and store them internally.

void SetOfActiveNetworks::computeNodeCounts ( )

For each node, compute how many ActiveNetworks it appears in.

void SetOfActiveNetworks::computeNodeSimilarityGraph ( MyGraph & graph ) const

Compute a graph representing the similarity of the node sets of the ActiveNetworks.

The method constructs a graph where each node is an active network and the weight of each edge is the set similarity of the node sets of the two active networks connected by the edge.

void SetOfActiveNetworks::computeNodeWeights ( const GEData & gedata )

Compute node weights in each ActiveNetwork.

Parameters:

[in] geData,a reference to a gene expression dataset.

void SetOfActiveNetworks::computePvalues ( const MyHistogram & histogram )

Compute p-values of ActiveNetworks from a histogram of densities in random networks.

Parameters:

[in] histogram,a histogram of densities in ActiveNetworks computed in random networks.

void SetOfActiveNetworks::computeSNetwork ( )

Compute the "s"Network formed by the ActiveNetworks.

An "s"Network ("s" stands for "state", "stimulus", "stress", or what have you) is a network where nodes are ActiveNetworks and edges represent similarities between ActiveNetworks. This method constructs the minimum spanning tree of the complete graph connecting all ActiveNetworks.

Note:: The method computes the set similarity between the edge sets of each pair of ActiveNetworks and uses 1 - the similarity as the edge weight.

void SetOfActiveNetworks::computeUnion	(	string	name,
		ActiveNetwork &	unionActiveNetwork
	)		`[inline]`

Compute the union of all ActiveNetworks.

Parameters:

[in]	name,a	string from which to form the name of the union.
[out]		unionActiveNetwork, an instance of ActiveNetwork that will contain the union.

void SetOfActiveNetworks::computeUnion ( string name )

Compute the union of all ActiveNetworks and store it internally.

Parameters:

[in] name,a string from which to form the name of the union.

void SetOfActiveNetworks::expand	(	const GEData &	expression,
		string	id,
		MyNT	correlationThreshold
	)

Expand computed ActiveNetworks using edges with high correlation that are not in the wiring diagram.

vector< ActiveNetwork > SetOfActiveNetworks::getActiveNetworks ( ) [inline]

Return the ActiveNetworks.

Parameters:

[out] _anets, a vector containing all the ActiveNetworks in the set.

void SetOfActiveNetworks::getUnion ( ActiveNetwork & unionActiveNetwork ) [inline]

Return the union of all ActiveNetworks.

Parameters:

[out] unionActiveNetwork, an instance of ActiveNetwork that will contain the union.

The method assumes that you have already invoked one of the versions of SetOfActiveNetworks::computeUnion().

void SetOfActiveNetworks::printEdgeWeightsHistograms	(	ostream &	edgeWeightsHistogramStream,
		string	fileName
	)

Print edge weight histograms to a file and run gnuplot on this file.

Parameters:

edgeWeightsHistogramStream,an	output stream to print the histograms to. This stream must be a file stream.
fileName,the	name of the file that the first parameter points to.

void SetOfActiveNetworks::printNodeWeightsHistograms	(	ostream &	nodeWeightsHistogramStream,
		string	fileName
	)

Print node weight histograms to a file and run gnuplot on this file.

Parameters:

nodeWeightsHistogramStream,an	output stream to print the histograms to. This stream must be a file stream.
fileName,the	name of the file that the first parameter points to.

void SetOfActiveNetworks::read ( const vector< string > & activeNetworkFiles )

Read ActiveNetworks from a list of files.

Parameters:

[in] activeNetworkFiles,a vector of strings.

See the documentation for ActiveNetworks::read(string) for more details.

void SetOfActiveNetworks::read ( string activeNetworkFile )

Read ActiveNetworks from a file.

Parameters:

[in] file,the name of a file containing ActiveNetworks.

The file contains ActiveNetworks stored in "itemset" format. Each line describes a single ActiveNetwork.

void SetOfActiveNetworks::readEdges ( string edgesFile )

Read edges in a set of ActiveNetworks from a file.

Parameters:

[in] edgesFile,a tab-delimited file containing all the edges in the ActiveNetworks. Each line contains the identifier of an ActiveNetwork, the identifiers of the two nodes incident on the edge, and the type of the edge.

virtual void SetOfActiveNetworks::readMappingFromNetworkLegosToActiveNetworks ( string nlsToRNsFile ) [inline, virtual]

This function is defined in SetOfActiveNetworks only because of an implementation detail in NetMan::processComputedActiveNetworks(). Ideally, this method should be defined only in SetOfNetworkLegos.

Reimplemented in SetOfNetworkLegos.

void SetOfActiveNetworks::readNodeEnrichedFunctions ( string nodeEnrichedFunctionsFile )

Read ActiveNetwork-node-enriched-function triples from a file.

Parameters:

[in] nodeEnrichedFunctionsFile,a tab-delimited file previously output by invoking SetOfActiveNetworks::printNodeEnrichedFunctions().

void SetOfActiveNetworks::readNodeEnrichments ( string nodeEnrichmentsFile )

Read ActiveNetwork-node-enriched-function p-values from a file.

Parameters:

[in] nodeEnrichmentsFile,a tab-delimited file previously output by invoking SetOfActiveNetworks::printNodeEnrichments().

void SetOfActiveNetworks::readNodes	(	string	nodesFile,
		MyGraph &	superGraph
	)

Read nodes in a set of ActiveNetworks from a file.

Parameters:

[in]	nodesFile	a tab-delimited file containing all the nodes in the ActiveNetworks. Each line contains the identifier of an ActiveNetwork and the identifier of one nodes in that ActiveNetwork.
[in]	superGraph	an instance of MyGraph of which the ActiveNetworks are subgraphs.

Note:: For each set of nodes in nodesFile, the method will create an ActiveNetwork that is the subgraph of superGraph induced by the node set.

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

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

Public Member Functions

Protected Attributes

Friends

Detailed Description

Member Function Documentation