Retreive and integrate the clustered Protein-Protein Interaction Network (PPIN) data

This function retrieves and reformats the clustered PPIN data from the StringApp in Cytoscape.

Usage

getclustrs(gene_data, colname_for_merge, path, nodetable_filename)

Arguments

gene_data: A dataframe of type t that typically corresponds to the output of the getids() or getregs() function. This input holds at least one column named "gene_id” holding gene identifiers for the deregulated genes.
colname_for_merge: The identifier column used as query in order to create the PPIN in Cytoscape using the StringApp (e.g. "ensembl_gene_id" or "uniprotsptrembl")
path: Folder where the nodetable exported from Cytoscape is found
nodetable_filename: Filename of the nodetable

Value

A dataframe of type t similar to the gene_data dataframe input with an added column indicating to which cluster belongs each gene (if no cluster is associated : NA)

Examples

if (FALSE) { # \dontrun{
# This function requires clustered Protein-Protein Interaction (PPI) Network data from Cytoscape
# 1. Export your gene IDs to STRING database in Cytoscape
# 2. Construct a PPI network
# 2. Apply MCL clustering (with params, for example, inflation = 4.0 and confidence score = 0.9)
# 3. Export node table as CSV

example_getclustrs_res <- getclustrs(
  gene_data = your_getregs_res, # OR your_getids_res
  colname_for_merge = "gene_id",
  path = "outputs/2025-08-21/cytoscape-files/",
  nodetable_filename = "string_clustered_network.csv"
)

# See package vignette for complete Cytoscape workflow
} # }