Calculation of the overlap of soft clusters

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Description

This function calculates the overlap of clusters produced by mfuzz.

Usage

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overlap(cl)

Arguments

cl

object of class flclust

Value

The function generates a matrix of the normalised overlap of soft clusters. The overlap indicates the extent of “shared” genes between clusters. For a mathematical definiton of the overlap, see the vignette of the package or the reference below.

Author(s)

Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)

References

M.E. Futschik and B. Charlisle, Noise robust clustering of gene expression time-course data, Journal of Bioinformatics and Computational Biology, 3 (4), 965-988, 2005

Examples

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if (interactive()){
data(yeast)
# Data pre-processing
yeastF <- filter.NA(yeast)
yeastF <- fill.NA(yeastF)
yeastF <- standardise(yeastF)

# Soft clustering and visualisation
cl <- mfuzz(yeastF,c=20,m=1.25)
mfuzz.plot(yeastF,cl=cl,mfrow=c(4,5))

# Calculation of cluster overlap and visualisation 
O <- overlap(cl)
X11()
Ptmp <- overlap.plot(cl,over=O,thres=0.05)
}

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