Generate geneset networks from an annotated network.

Source: R/netWeight.R

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")
)

Arguments

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.

Value

A list of geneset networks as igraph or Pathway-class objects.

See also

getGeneSets

Author

Ahmed Mohamed

Examples

 data(ex_kgml_sig)  # Ras and chemokine signaling pathways in human
 genesetnets <- getGeneSetNetworks(ex_kgml_sig, use.attr="pathway")
#> This graph was created by an old(er) igraph version.
#> ℹ Call `igraph::upgrade_graph()` on it to use with the current igraph version.
#> For now we convert it on the fly...

 # Integration with graphite package
 if (FALSE) { # \dontrun{
 if(requireNamespace("graphite") & requireNamespace("clipper") & requireNamespace("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)
 }
 } # }