graphite (version 1.12.0)

runTopologyGSA: 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

runTopologyGSA(pathway, test, exp1, exp2, alpha, ...)

Arguments

pathway

One of the pathways contained in biocarta, kegg,nci or reactome.

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.

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

if (require(topologyGSA)) {
  data(examples)

  p <- convertIdentifiers(kegg[["Fc epsilon RI signaling pathway"]], "symbol")
  runTopologyGSA(p, "var", y1, y2, 0.05)
}