calculate_interaction_score {DrDimont}

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

Description

[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.

Usage

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)

Value

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