runTopologyGSA {graphite} | R Documentation |
Use graphical models to test the pathway components highlighting those involved in its deregulation.
runTopologyGSA(x, test, exp1, exp2, alpha, ...)
x |
a |
test |
Either |
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 When invoked on a |
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.
Massa MS, Chiogna M, Romualdi C. Gene set analysis exploiting the topology of a pathway. BMC System Biol. 2010 Sep 1;4:121.
pathway.var.test
pathway.mean.test
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) }