MEGENA (version 1.3.7)

get.union.cut: Scale-thresholding of multiscale modules.

Description

obtain a discrete, disjoint clustering results from multiscale MEGENA modules for a given alpha value.

Usage

get.union.cut(module.output,alpha.cut,output.plot = T,
plotfname = "validModules_alpha",module.pval = 0.05,remove.unsig = T)

Arguments

module.output

A direct output from "do.MEGENA". (i.e. MEGENA.output$module.output).

alpha.cut

Resolution parameter cut-off (i.e. alpha) value. alpha.cut = 1 corresponds to classical definition of "small-world" compactness.

output.plot

TRUE/FALSE to indicate outputting a .png file showing hierarchical structure with final outputted modules highlighted in red.

plotfname

.png file outputname.

module.pval

module significance p-value.

remove.unsig

TRUE/FALSE indicating to remove insignificant clusters.

Details

Returns a list object where each entry is a module.

Examples

# NOT RUN {
rm(list = ls())
data(Sample_Expression)
ijw <- calculate.correlation(datExpr[1:100,],doPerm = 2)
el <- calculate.PFN(ijw[,1:3])
g <- graph.data.frame(el,directed = FALSE)
MEGENA.output <- do.MEGENA(g = g,remove.unsig = FALSE,doPar = FALSE,n.perm = 10)
get.union.cut(module.output = MEGENA.output$module.output,alpha.cut = 1,
output.plot = FALSE,plotfname = NULL,module.pval = 0.05,remove.unsig = TRUE)
# }