getGeneSets {NetPathMiner} | R Documentation |
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)
graph |
An annotated igraph object.. |
use.attr |
The attribute by which vertices are grouped (tepically pathway, or GO) |
gene.attr |
The attribute listing genes annotated with each vertex (ex: miriam.ncbigene, miriam.uniprot, ...) |
gmt.file |
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.
Ahmed Mohamed
data(ex_kgml_sig) # Ras and chemokine signaling pathways in human genesets <- getGeneSets(ex_kgml_sig, use.attr="pathway", gene.attr="miriam.ncbigene") # 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") ## Not run: if(require(GSEABase)) toGmt("kgml.gmt") ## End(Not run) # 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")