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Harmonize gene and PTM node tables for a combined CFN/CCCN network

Source: R/CytoscapeGraphingFunctions.R
harmonize_cfs.Rd

Merges a gene-level node attribute table with PTM-level rows derived from the PTM table, ensuring the id column is present and used as the Cytoscape node key. PTM nodes are annotated from the function key and linked to their parent genes via a parent column.

Usage

harmonize_cfs(edge.file.with.ptms, genecf, ptmtable)

Arguments

edge.file.with.ptms

A data frame edge list containing both gene and PTM (interaction == "peptide") edges.

genecf

A gene-level node attribute data frame, typically produced by make.cytoscape.node.file.

ptmtable

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

Value

A merged data frame of gene and PTM node attributes with id as the first column, suitable for RCy3::createNetworkFromDataFrames.