pathCluster: 3M Markov mixture model for clustering pathways

In aiminy/NetPathMiner: NetPathMiner for Biological Network Construction, Path Mining and Visualization

Description

3M Markov mixture model for clustering pathways

Usage

pathCluster(ybinpaths, M, iter = 1000)

Arguments

ybinpaths	The training paths computed by pathsToBinary.
M	The number of clusters.
iter	The maximum number of EM iterations.

Value

A list with the following items:

h	The posterior probabilities that each path belongs to each cluster.
labels	The cluster membership labels.
theta	The probabilities of each gene for each cluster.
proportions	The mixing proportions of each path.
likelihood	The likelihood convergence history.
params	The specific parameters used.

Author(s)

Ichigaku Takigawa

Timothy Hancock

References

Mamitsuka, H., Okuno, Y., and Yamaguchi, A. 2003. Mining biologically active patterns in metabolic pathways using microarray expression profiles. SIGKDD Explor. News l. 5, 2 (Dec. 2003), 113-121.

See Also

Other Path clustering & classification methods: pathClassifier, pathsToBinary, plotClassifierROC, plotClusterMatrix, plotPathClassifier, plotPathCluster, predictPathClassifier, predictPathCluster

Examples

	## Prepare a weighted reaction network.
	## Conver a metabolic network to a reaction network.
 data(ex_sbml) # bipartite metabolic network of Carbohydrate metabolism.
 rgraph <- makeReactionNetwork(ex_sbml, simplify=TRUE)

	## Assign edge weights based on Affymetrix attributes and microarray dataset.
 # Calculate Pearson's correlation.
	data(ex_microarray)	# Part of ALL dataset.
	rgraph <- assignEdgeWeights(microarray = ex_microarray, graph = rgraph,
		weight.method = "cor", use.attr="miriam.uniprot", bootstrap = FALSE)

	## Get ranked paths using probabilistic shortest paths.
 ranked.p <- pathRanker(rgraph, method="prob.shortest.path", 
					K=20, minPathSize=8)
	
	## Convert paths to binary matrix. 
	ybinpaths <- pathsToBinary(ranked.p)
	p.cluster <- pathCluster(ybinpaths, M=2)
	plotClusters(ybinpaths, p.cluster)
 

aiminy/NetPathMiner documentation built on May 12, 2019, 3:38 a.m.