Calculation of the overlap of soft clusters
This function calculates the overlap of clusters
produced by mfuzz.
overlap(cl)
cl |
object of class flclust |
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.
Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)
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
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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