graph (version 1.50.0)

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

Description

This function is deprecated and will be removed in a future release. You can use runDEGraph instead.

Usage

runDEGraphMulti(pathways, expr, classes, maxNodes=150)

Arguments

pathways

a PathwayList 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.

maxNodes

Ignore pathways with more than "maxNodes" nodes. Set to NULL to disable the filter.

Value

• A list with two elements:
  • results
  : a list with one entry for each successfully analyzed pathway;
• errors
• : a vector containing the error messages of failed analyses.

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

Examples

if (require(DEGraph)) {
  data("Loi2008_DEGraphVignette")

  b <- pathways("hsapiens", "biocarta")
  ps <- convertIdentifiers(b[1:3], "entrez")
  runDEGraphMulti(ps, exprLoi2008, classLoi2008)
}