graphite (version 1.12.0)

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

Description

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

Usage

runTopologyGSAMulti(pathways, test, exp1, exp2, alpha, maxNodes=150, ...)

Arguments

pathways

A list of pathways, such as 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.

maxNodes

Ignore pathways with more than "maxNodes" nodes. Set to "NULL" to disable the filter.

...

Additional parameters for topologyGSA.

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

This function produces a warning and whenever the number of genes in common between the expression matrices and a 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)

  ps <- lapply(kegg[c("Acute myeloid leukemia", "Fc epsilon RI signaling pathway")],
               function(p) convertIdentifiers(p, "symbol"))
  runTopologyGSAMulti(ps, "var", y1, y2, 0.05)
}