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)