runDEGraph:
Run a topological analysis on an expression dataset using DEGraph package.
Description
DEGraph implements recent hypothesis testing methods which directly
assess whether a particular gene network is differentially expressed
between two conditions.
A matrix (size: number p of genes x number n of
samples) of gene expression.
classes
A vector (length: n) of class assignments.
Details
The expression data and the pathway have to be annotated in the same set of identifiers.
References
L. Jacob, P. Neuvial, and S. Dudoit. Gains in power from structured
two-sample tests of means on graphs. Technical Report
arXiv:q-bio/1009.5173v1, arXiv, 2010.
if (require(DEGraph)) {
data("Loi2008_DEGraphVignette")
p <- convertIdentifiers(biocarta[["actions of nitric oxide in the heart"]], "entrez")
runDEGraph(p, exprLoi2008, classLoi2008)
}