score_drugs_distance_based: Distance-based Scoring of Drugs

In egeulgen/PANACEA: Personalized Network-Based Anti-Cancer Therapy Evaluation

Distance-based Scoring of Drugs

Description

Distance-based Scoring of Drugs

Usage

score_drugs_distance_based(
  driveR_res,
  drug_interactions_df,
  W_mat,
  driver_prob_cutoff = 0.05,
  drug_name_col = "drug_name",
  target_col = "gene_name",
  verbose = TRUE
)

Arguments

driveR_res	data frame of driveR results
drug_interactions_df	data frame of drug-gene interactions
W_mat	adjacency matrix for the PIN
driver_prob_cutoff	cut-off value for 'driverness_prob' (default = 0.05)
drug_name_col	for 'drug_interactions_df', the column name containing drug names/identifiers
target_col	for 'drug_interactions_df', the column name containing target gene symbols
verbose	boolean to control verbosity (default = TRUE)

Value

vector of scores per drug. Drugs with the same target gene(s) are merged (via process_drug_target_interactions)

Examples

toy_data <- data.frame(
  gene_symbol = c("TP53", "EGFR", "KDR", "ATM"),
  driverness_prob = c(0.94, 0.92, 0.84, 0.72)
)
toy_interactions <- DGIdb_interactions_df[1:100, ]
res <- score_drugs_distance_based(
  driveR_res = toy_data,
  drug_interactions_df = toy_interactions,
  W_mat = toy_W_mat, verbose = FALSE
)

egeulgen/PANACEA documentation built on Aug. 20, 2023, 7:28 a.m.