getGeneSetNetworks {NetPathMiner} | R Documentation |
This function generates geneset networks based on a given netowrk, by grouping vertices sharing common attributes (in the same pathway or compartment).
getGeneSetNetworks(graph, use.attr = "pathway", format = c("list", "pathway-class"))
graph |
An annotated igraph object.. |
use.attr |
The attribute by which vertices are grouped (tepically pathway, or GO) |
format |
The output format. If "list" is specified, a list of subgraphs are returned (default). If "pathway-class" is specified, a list of pathway-class objects are returned. Pathway-class is used by graphite package to run several methods of topology-based enrichment analyses. |
A list of geneset networks as igraph or Pathway-class objects.
Ahmed Mohamed
data(ex_kgml_sig) # Ras and chemokine signaling pathways in human genesetnets <- getGeneSetNetworks(ex_kgml_sig, use.attr="pathway") # Integration with graphite package ## Not run: if(require(graphite) & require(clipper) & require(ALL)){ genesetnets <- getGeneSetNetworks(ex_kgml_sig, use.attr="pathway", format="pathway-class") path <- convertIdentifiers(genesetnets$`Chemokine signaling pathway`, "entrez") genes <- nodes(path) data(ALL) all <- as.matrix(exprs(ALL[1:length(genes),1:20])) classes <- c(rep(1,10), rep(2,10)) rownames(all) <- genes runClipper(path, all, classes, "mean", pathThr=0.1) } ## End(Not run)