runDEGraph

Run a topological analysis on an expression dataset using DEGraph package.

DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions.

Keywords
analysis, topology, DEGraph
Usage
runDEGraph(x, expr, classes, ...)
Arguments
x
a PathwayList, a list of Pathways or a single Pathway object.
expr
a matrix (size: number p of genes x number n of samples) of gene expression.
classes
a vector (length: n) of class assignments.
...
when invoked on a PathwayList, can use the named option "maxNodes" to limit the analysis to those pathways having up to this given number of nodes.
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.

See Also

testOneGraph

Aliases
  • runDEGraph
  • runDEGraph,list-method
Examples
if (require(DEGraph)) {
  data("Loi2008_DEGraphVignette")

  b <- pathways("hsapiens", "biocarta")
  p <- convertIdentifiers(b[["actions of nitric oxide in the heart"]], "entrez")
  runDEGraph(p, exprLoi2008, classLoi2008)
}
Documentation reproduced from package graph, version 1.50.0, License: Artistic-2.0

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