Description Usage Arguments Details Value Author(s) References Examples
The biclust package implements several biclustering
algorithms in a unified framework. The result of the biclustering is a
Biclust
object. These functions allow the
conversion between Biclust
and
ISAModules
objects.
1 |
biclusters |
A |
data |
An |
To convert an ISAModules
object (mods
) to a
Biclust
object (bc
), you can do:
1 2 | bc <- as(mods, "Biclust")
|
The seed data and run data of the ISAModules
object is stored
in the Parameters
slot of the Biclust
object. The ISA
scores are binarized by the conversion.
To convert a Biclust
object (bc
) to an ISAModules
object (mods
), you can call:
1 2 | mods <- as(bc, "ISAModules")
|
The Parameters
slot of the Biclust
object is used as the
run data of the ISAModules
object. The seed data of the new
object will be an empty data frame.
The annotate
function puts biological annotation into a
Biclust
object. It is suggested to use it before converting the
Biclust
object to ISAModules
, so that ISA visualization
functions and enrichment calculations can make use of this information.
annotate
returns a Biclust
object.
Gabor Csardi csardi.gabor@gmail.com
Bergmann S, Ihmels J, Barkai N: Iterative signature algorithm for the analysis of large-scale gene expression data Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Mar;67(3 Pt 1):031902. Epub 2003 Mar 11.
Sebastian Kaiser, Rodrigo Santamaria, Roberto Theron, Luis Quintales and Friedrich Leisch. (2009). biclust: BiCluster Algorithms. R package version 0.8.1. http://CRAN.R-project.org/package=biclust
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 | if (require(biclust)) {
library(ALL)
data(ALL)
ALL.filtered <- ALL[sample(1:nrow(ALL), 1000),]
# Biclust -> ISAModules
set.seed(1)
Bc <- biclust(exprs(ALL.filtered), BCPlaid(),
fit.model = ~m + a + b, verbose = FALSE)
Bc <- annotate(Bc, ALL.filtered)
modules <- as(Bc, "ISAModules")
Bc
modules
getNoFeatures(modules)
getNoSamples(modules)
# ISAModules -> Biclust
data(ALLModulesSmall)
Bc2 <- as(ALLModulesSmall, "Biclust")
ALLModulesSmall
getNoFeatures(ALLModulesSmall)
getNoSamples(ALLModulesSmall)
Bc2
}
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.