This function generates genesets based on a given netowrk, by grouping vertices sharing
common attributes (in the same pathway or compartment). Genes associated with each vertex
can be specified through gene.attr argument.
getGeneSets(graph, use.attr = "pathway", gene.attr = "genes", gmt.file)An annotated igraph object..
The attribute by which vertices are grouped (tepically pathway, or GO)
The attribute listing genes annotated with each vertex (ex: miriam.ncbigene, miriam.uniprot, ...)
Optinal. If provided, Results are exported to a GMT file. GMT files are readily used by most gene set analysis packages.
A list of genesets or written to gmt file if provided.
data(ex_kgml_sig) # Ras and chemokine signaling pathways in human
genesets <- getGeneSets(ex_kgml_sig, use.attr="pathway", gene.attr="miriam.ncbigene")
#> 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...
# Write the genesets in a GMT file, and read it using GSEABase package.
getGeneSets(ex_kgml_sig, use.attr="pathway", gene.attr="miriam.ncbigene", gmt.file="kgml.gmt")
if (FALSE) { # \dontrun{
if(requireNamespace("GSEABase"))
toGmt("kgml.gmt")
} # }
# Create genesets using compartment information
data(ex_sbml) # bipartite metabolic network of Carbohydrate metabolism.
genesets <- getGeneSets(ex_sbml, use.attr="compartment.name", gene.attr="miriam.uniprot")
#> 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...