runDEGraphMulti

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

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

Keywords
analysis, topology
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.
Details

The expression data and the pathway have to be annotated in the same set of identifiers.

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.

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
  • runDEGraphMulti
Examples
if (require(DEGraph)) {
  data("Loi2008_DEGraphVignette")

  b <- pathways("hsapiens", "biocarta")
  ps <- convertIdentifiers(b[1:3], "entrez")
  runDEGraphMulti(ps, exprLoi2008, classLoi2008)
}
Documentation reproduced from package graph, version 1.50.0, License: Artistic-2.0

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