graphite (version 1.12.0)

runDEGraphMulti: Run topological analyses on an expression dataset, calling DEGraph over all the pathways in a list.

Description

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

Usage

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

Arguments

pathways

A list of pathways, such as biocarta, kegg,nci or reactome.

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")

  ps <- lapply(biocarta[1:3],
               function(p) convertIdentifiers(p, "entrez"))
  runDEGraphMulti(ps, exprLoi2008, classLoi2008)
}