Get Kinase-Substrate Edges

Read a kinase-substrate dataset from PhosphoSitePlus and return an edge list filtered to the supplied node set. Optionally standardizes the node list using a precomputed symbol map.

Usage

GetKinsub.edges(
  kinasesubstrate.filename = "Kinase_Substrate_Dataset.txt",
  gene.cccn.nodes,
  symbol.map = NULL
)

Arguments

kinasesubstrate.filename

Path to the kinase substrate database file.

gene.cccn.nodes

Character vector of CCCN node symbols.

symbol.map

Optional data frame produced by StandardizeGeneSymbols(). If supplied, gene.cccn.nodes will be converted to standard_symbol before filtering.

Value

Data frame with columns: source, target, interaction, Weight

Examples

# sym.map <- StandardizeGeneSymbols(ex.gene.cccn.nodes)
# ks.edges <- GetKinsub.edges(
#   kinasesubstrate.filename = "Kinase_Substrate_Dataset.txt",
#   gene.cccn.nodes = ex.gene.cccn.nodes,
#   symbol.map = sym.map
# )