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

Description Usage Arguments Details Value References See Also Examples

View source: R/degraph.R

Description

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

Usage

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  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:

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

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

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

graphite documentation built on May 31, 2017, 3:20 p.m.