CPBADecomposition: Cluster and Propensity-based Approximation decomposition for...

Description Usage Arguments Details Value Author(s) References See Also Examples

Description

Given an adjacency matrix and cluster assignments, this function calculates either the conformity factors or the propensities of each node.

Usage

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CPBADecomposition(adjacency,
                  clustering,
                  nClusters = NULL,
                  objectiveFunction = c("Poisson", "L2norm"),
                  dropUnassigned = TRUE,
                  unassignedLabel = 0,
                  unassignedMethod = "average",
                  accelerated = TRUE,
                  parallel = FALSE)

Arguments

adjacency

A square symmetric matrix giving either the number of connections between two nodes (for Poisson objective function) or the weighted connections (between 0 and 1) between each pair of nodes.

clustering

A vector with element per node containing the cluster assignments for each node. If a single cluster decomposition is desired, an alternative is to set nClusters=1 (see below).

nClusters

If the user wishes to input trivial clustering to calculate a "pure propensity" decomposition, this variable can be set to 1. Any other non-NULL value is considered invalid; use clusters to specify a non-trivial clustering.

objectiveFunction

Specifies the objective function for the Cluster and Propensity-based Approximation. Valid choices are (unique abbreviations of) "Poisson" and "L2norm".

dropUnassigned

Logical: should unassigned nodes be excluded from the clustering? Unassigned nodes can be present in initial clustering or blocks (if given), and internal pre-partitioning and initial clustering can also lead to unassigned nodes. If dropUnassigned is TRUE, these nodes are excluded from the calls to propensityClustering. Otherwise these nodes will be assigned to the nearest cluster within each block and be clustered using propensityClustering in each block.

unassignedLabel

Label in input clustering that is reserved for unassigned objects. For clusterings with numeric lables this is typically (but not always) 0. Note that this must a valid value - missing value NA will not work.

unassignedMethod

If dropUnassigned is FALSE, this argument sepcifies the method to assign unassigned objects to the nearest cluster. Valid values are (unique abbreviations) of "average", "single", and "complete". In analogy with hierarchical clustering, each node will be assigned to the cluster with which it has the highest average, maximum, and minimum adjacency, respectively.

accelerated

Logical: should an accelerated algorithm be used? In general the accelerated method is preferable.

parallel

Logical: should parallel calculation be used? At present the parallel calculation is not fully implemented and the function falls back to standard accelerated calculation, with a warning.

Details

If a single cluster is specified, the approximation is known as "Pure Propensity".

If unassigned nodes are present in the clustering and they are dropped before the CPBA calculation, their propensities, mean values and tail p-values are returned as NA.

Value

Returns the following list of items.

Propensity

Gives the propensities (or conformities) of each node.

IntermodularAdjacency

Gives the intermodular adjacencies or the conformities between clusters.

Factorizability

Gives the factorizability of the data.

L2Norm or Loglik

The L2 Norm (for L2 norm objective function) or the log-likelihood (for Poisson objetive function).

ExpectedAdjancency

A distance structure representing the lower triangle of the symmetric matrix of estimated values of the adjacency matrix using the Propensity and IntermodularAdjacency. If the Poisson updates are used, the returned values are the estimate means of the distribution.

EdgePvalues

A distance structure representing the lower triangle of the symmetric matrix of the tail probabilities under the Poisson distribution.

Author(s)

John Michael Ranola, Peter Langfelder, Steve Horvath, Kenneth Lange

References

Ranola et. al. (2010) A Poisson Model for Random Multigraphs. Bioinformatics 26(16):2004-2001. Ranola JM, Langfelder P, Lange K, Horvath S (2013) Cluster and propensity based approximation of a network. BMC Bioinformatics, in press.

See Also

propensityClustering

Examples

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nNodes=50
nClusters=5
#We would like to use L2Norm instead of Loglikelihood
objective = "L2norm"

ADJ<-matrix(runif(nNodes*nNodes),ncol=nNodes)
for(i in 1:(length(ADJ[1,])-1)){
		for(j in i:length(ADJ[,1])){
			ADJ[i,j]=ADJ[j,i]
		}
	}

for(i in 1:length(ADJ[1,])) ADJ[i,i]=0 

Results<-propensityClustering(
              adjacency = ADJ,
              objectiveFunction = objective,
              initialClusters = NULL,
              nClusters = nClusters,
              fastUpdates = FALSE)

Results2<-CPBADecomposition(adjacency = ADJ, clustering = Results$Clustering, 
                            objectiveFunction = objective)

Results3<-propensityClustering( adjacency = ADJ,
              objectiveFunction = objective,
              initialClusters = NULL,
              nClusters = nClusters,
              fastUpdates = TRUE)

PropClust documentation built on May 1, 2019, 9:44 p.m.