runTopologyGSA: Run a topological analysis on an expression dataset using...

In graphite: GRAPH Interaction from pathway Topological Environment

Description

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

If the option Ncpus is set to a value larger than 1 and the package parallel is installed, the conversion procedure will automatically use multiple cores.

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

Examples

if (require(topologyGSA)) {
  data(examples)
  colnames(y1) <- paste("SYMBOL", colnames(y1), sep = ":")
  colnames(y2) <- paste("SYMBOL", colnames(y2), sep = ":")

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

Example output

Loading required package: topologyGSA
No methods found in package ‘GenomicRanges’ for request: ‘c’ when loading ‘qpgraph’
Error: package or namespace load failed for ‘topologyGSA’:
 memory exhausted (limit reached?)
Warning message:
system call failed: Cannot allocate memory 

graphite documentation built on Nov. 8, 2020, 8:12 p.m.