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Build Pathway Crosstalk Network

BuildPathwayCrosstalkNetwork.Rd

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.

Usage

BuildPathwayCrosstalkNetwork(
  common.clusters,
  bioplanet.file = "bioplanet.csv",
  createfile = getwd(),
  PCN.edgelist.name = "PCN_file"
)

Arguments

common.clusters

The list of common clusters between all three distance metrics (Euclidean, Spearman, and SED). Can be made in MakeCorrelationNetwork

bioplanet.file

Either the name of the bioplanet pathway .csv file OR a dataframe. Lines of bioplanet should possess 4 values in the order "PATHWAY_ID","PATHWAY_NAME","GENE_ID","GENE_SYMBOL". Users not well versed in R should only pass in "yourfilename.csv"

createfile

The path of where to create the edgelist file. Defaults to the working directory, if FALSE is provided, a file will not be created.

Value

A list with these data structures at the given index:

  1. Contains pathway source-target columns, along with the interaction type.

  2. Contains pathway source-target columns, with edge weights of their jaccard similarity and their Pathway-Pathway Evidence score.

  3. All pathways in the bioplanet database as a named list containing string vectors. Each vector is a pathway with strings associated with the genes in that pathway.

Examples

Example_Output <- BuildPathwayCrosstalkNetwork(ex.common.clusters, ex.bioplanet, createfile = FALSE)
#> [1] "Making PCN"
#> [1] "2026-03-25 23:11:58 UTC"
#> Error: object 'ex.bioplanet' not found
Example_Output[[1]][[3,]]
#> Error: object 'Example_Output' not found
Example_Output[[3]][[1:3]]
#> Error: object 'Example_Output' not found