isa.biclust {isa2} | R Documentation |
Convert ISA modules to a Biclust class, as defined by the biclust package
Description
This function converts the object with ISA modules to a Biclust
object, so all the functions in the biclust
package can be used
on it.
Usage
isa.biclust(modules)
Arguments
modules |
The ISA modules, as returned by the |
Details
biclust
is an R package that implements many biclustering
algorithms in a unified framework. This function converts a set of ISA
biclusters to a Biclust
object, this class is used to store all
biclustering results by the biclust
package.
The Biclust
class only supports binary biclusters, so the ISA
modules are binarized during the conversion.
Value
A Biclust
object.
Author(s)
Gabor Csardi Gabor.Csardi@unil.ch
Examples
## You need the biclust package for this
## Not run:
if (require(biclust)) {
set.seed(1)
data <- isa.in.silico()
modules <- isa(data[[1]])
bc <- isa.biclust(modules)
## A heatmap
drawHeatmap(data[[1]], bc, 1)
## A "bubble" plot
bubbleplot(data[[1]], bc)
## Compare values inside and outside the bicluster
plotclust(bc, data[[1]])
## Plot profiles of bicluster elements
parallelCoordinates(data[[1]], bc, number=1)
## Coherence measures vs. ISA robustness
cV <- sapply(seq(bc@Number), function(x)
constantVariance(data[[1]], bc, x, dimension="both"))
aV <- sapply(seq(bc@Number), function(x)
additiveVariance(data[[1]], bc, x, dimension="both"))
mV <- sapply(seq(bc@Number), function(x)
multiplicativeVariance(data[[1]], bc, x, dimension="both"))
sV <- sapply(seq(bc@Number), function(x)
signVariance(data[[1]], bc, x, dimension="both"))
rob <- robustness(isa.normalize(data[[1]]), modules$rows,
modules$columns)
cor( cbind(cV, aV, mV, sV, rob) )
}
## End(Not run)
[Package isa2 version 0.3.6 Index]