calculate_interaction_score: Calls a python script to calculate interaction score for...

In molnet-org/molnet: Predicting Differential Drug Response using Multi-Omics Networks

Description

(INTERNAL) The interaction score is computed and replaces the edge weight. This function expects the combined graphs for both groups along with their corresponding drug target and node lists to be present at 'loading_path'. Graphs and drug targets should be weighted edge lists in tsv format. 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,
  loading_path,
  python_executable = "python3",
  script_path = NULL,
  int_score_mode = "auto"
)

Arguments

max_path_length	The maximum length of simple paths to consider when computing the interaction score
total_edges	vector with total edges in each group
loading_path	Directory to use for writing intermediate data when passing input and output between Python and R
python_executable	Python command or path to Python executable to use
script_path	Path to the interaction score Python script. Set NULL to use package internal script (default).
int_score_mode	One of 'auto', 'sequential' or 'ray'. Whether to compute interaction score in parallel using the Ray python library or sequentially. When 'auto' it depends on the graph sizes.

molnet-org/molnet documentation built on Dec. 21, 2021, 8:59 p.m.