Run a topological analysis on an expression dataset using topologyGSA.

Description

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

Usage

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  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

Examples

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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)
}