Mfuzz (version 2.32.0)

overlap: Calculation of the overlap of soft clusters

Description

This function calculates the overlap of clusters produced by mfuzz.

Usage

overlap(cl)

Arguments

cl

object of class flclust

Value

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.

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

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)
}