Build a Cytoscape node attribute table from an edge file

Extracts unique gene nodes from an edge file, annotates them using the function key, and optionally appends gene-level PTM data and co-clustered PTM nodes.

Usage

make.cytoscape.node.file(
  edge.file,
  funckey = PTMsToPathways::function_key,
  ptmtable,
  include.gene.data = FALSE,
  include.coclustered.PTMs = FALSE,
  ptm.cccn.edges = NULL
)

Arguments

edge.file

A data frame edge list with node names in columns 1 and 2 and an interaction column.

funckey

A data frame mapping gene names to protein annotations (e.g., PTMsToPathways::function_key).

ptmtable

A PTM data frame with PTM identifiers as row names and numeric condition columns.

include.gene.data

Logical; if TRUE, append gene-level summarised PTM values to the node table. Defaults to FALSE.

include.coclustered.PTMs

Logical; if TRUE, add co-clustered PTM nodes and their edges to the output. Defaults to FALSE.

ptm.cccn.edges

A data frame of PTM co-expression correlation network edges with PTM identifiers as node names, required if include.coclustered.PTMs = TRUE.

Value

A data frame of node attributes with an id column suitable for RCy3::createNetworkFromDataFrames.