runTopologyGSA

Run a topological analysis on an expression dataset using topologyGSA.

Use graphical models to test the pathway components highlighting those involved in its deregulation.

Keywords
analysis, topology, topologyGSEA
Usage
runTopologyGSA(x, test, exp1, exp2, alpha, ...)
Arguments
x
a PathwayList, a list of Pathways or a single Pathway object.
test
Either "var" and "mean". Determine the type of test used by topologyGSA.
exp1
Experiment matrix of the first class, genes in columns.
exp2
Experiment matrix of the second class, genes in columns.
alpha
Significance level of the test.
...
Additional parameters forwarded to topologyGSA.

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

This function produces a warning and returns NULL when the number of genes in common between the expression matrices and the pathway is less than 3.

References

Massa MS, Chiogna M, Romualdi C. Gene set analysis exploiting the topology of a pathway. BMC System Biol. 2010 Sep 1;4:121.

See Also

pathway.var.test pathway.mean.test

Aliases
  • runTopologyGSA
  • runTopologyGSA,list-method
Examples
if (require(topologyGSA)) {
  data(examples)

  k <- pathways("hsapiens", "kegg")
  p <- convertIdentifiers(k[["Fc epsilon RI signaling pathway"]], "symbol")
  runTopologyGSA(p, "var", y1, y2, 0.05)
}
Documentation reproduced from package graph, version 1.50.0, License: Artistic-2.0

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