calculate_interaction_score function

[INTERNAL] Calls a python script to calculate interaction score for combined graphs

[INTERNAL] The interaction score is computed and saved in an additional interaction_weight edge attribute. This function expects the combined graphs for both groups along with their corresponding drug target and node lists to be saved at saving_path. Graphs and drug targets should be weighted edge lists in gml and tsv format, respectively. Node files should contain one node id per line. The script for calculating the interaction score is called with python_executable. An alternate script can be specified with script_path. The score for an edge is computed as the sum of the average product of weights along all simple paths of length l (over all path lengths up to max_path_length) between the source and target node of the edge.

calculate_interaction_score(
  max_path_length,
  total_edges,
  saving_path,
  conda = FALSE,
  script_path = NULL,
  int_score_mode = "auto",
  cluster_address = "auto",
  graphB_null = FALSE
)

Arguments

• max_path_length: [int] Integer of maximum length of simple paths to include in the generate_interaction_score_graphs computation. (default: 3)
• total_edges: Vector with total edges in each group
• saving_path: [string] Path to save intermediate output of DrDimont's functions. Default is current working directory. Directory to use for writing intermediate data when passing input and output between Python and R.
• conda: [bool] Specifying if python is installed in a conda environment. Set TRUE if python is installed with conda, else python dependencies are assumed to be installed with pip. (default: FALSE)
• script_path: [string] Path to the interaction score Python script. Set NULL to use package internal script (default).
• int_score_mode: ["auto"|"sequential"|"ray"] Whether to compute interaction score in parallel using the Ray python library or sequentially. When auto it depends on the graph sizes. (default: "auto")
• cluster_address: [string] Local node IP-address of Ray if executed on a cluster. On a cluster: Start ray with ray start --head --num-cpus 32 on the console before DrDimont execution. It should work with "auto", if it does not specify IP-address given by the ray start command. (default: "auto")
• graphB_null: [bool] Specifying if graphB of groupB is given (FALSE) or not (TRUE). (default: FALSE)

Returns

Does not return anything, instead calls Python script which outputs gml files