Subsets the PTM CCCN to the PTMs belonging to genes present in
edge.file, then appends gene-to-peptide edges so the result
can be directly used as an extended edge list in Cytoscape.
Usage
get.co.clustered.ptms(edge.file, ptm.cccn.edges, ptmtable)
Arguments
- edge.file
A data frame edge list whose nodes are gene names.
- ptm.cccn.edges
A data frame of PTM co-expression correlation network
edges with PTM identifiers as node names.
- ptmtable
A PTM data frame with PTM identifiers as row names and numeric condition columns.
Value
An edge data frame combining the original gene edges, co-clustered
PTM edges, and gene-to-peptide linking edges.
