if (FALSE) {
## load the data
data("breastcancer2012_subset")
## consider genes from just 2 pathways
genenames <- unique(c(pathways[["Adipocytokine signaling pathway"]],
pathways[["Adrenergic signaling in cardiomyocytes"]]))
sx <- x[match(rownames(x), genenames, nomatch = 0L) > 0L,]
db_edges <- obtainEdgeList(rownames(sx), databases = c("kegg", "reactome"))
adj_cluster <- prepareAdjMat(sx, group, databases = db_edges, cluster = TRUE)
out_cluster <- NetGSA(adj_cluster[["Adj"]], sx, group,
pathways_mat[c(1,2), rownames(sx)], lklMethod = "REHE", sampling = FALSE)
plot(out_cluster)
formatPathways(out_netgsa, "Adipocytokine signaling pathway")
}
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