R: Convert ISA modules to a Biclust class, as defined by the...

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 `isa` or some other function.

### 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 0.3.5 Index]