Pathway Crosstalk Network — PathwayCrosstalkNetwork • cccn.cfn.tools

Converts Bioplanet pathways from (https://tripod.nih.gov/bioplanet/) into a list of pathways whose elements are the genes in each pathway. Edge weights are either the PTM Cluster Weight or according to the Jaccard Similarity.

PathwayCrosstalkNetwork(
  file = "bioplanet.csv",
  clusterlist,
  edgelist.name = "edgelist"
)

Arguments

file: Either the name of the bioplanet pathway .csv file OR the name of a dataframe. Lines of bioplanet should possess 4 values in the order "PATHWAY_ID","PATHWAY_NAME","GENE_ID","GENE_SYMBOL". Users should only pass in "yourfilename.csv"
clusterlist: The list of coclusters made in MakeCorrelationNetwork
edgelist: The desired name for the edgelist file that PCN will make. Should NOT contain any file extensions like .csv, this step will add that for you. Intended for graphing in Cytoscape.

Examples

PathwayCrosstalkNetwork(ex.bioplanet, ex.common.clusters)
#> edgelist.csv made in directory: /home/runner/work/CCCN_CFN_Tools/CCCN_CFN_Tools/docs/reference