Constructs a metabolic interaction network tailored to the analyzed dataset. The function integrates network topology with gene–enzyme–reaction annotations, removes filtered metabolites, and retains only genes present in the processed expression matrix. Networks can be represented at either the metabolite or atom level. The final output corresponds to the largest connected component of the metabolic network and serves as the graph structure for GAM-clustering.
Usage
prepareNetwork(
E,
network,
topology = c("metabolites", "atoms"),
met.to.filter = data.table::fread(system.file("mets2mask.lst", package =
"GAMclust"))$ID,
network.annotation,
gene2reaction.extra = NULL
)Arguments
- E
Expression matrix after the
prepareData()function.- network
Metabolic network.
- topology
Vertices can be represented either as
metabolites, either asatoms.- met.to.filter
Metabolites that should not be used as connections in the module.
- network.annotation
Metabolic network annotation.
- gene2reaction.extra
For a combined network: supplementary file with genes that either come from proteome or are not linked to a specific enzyme.