PANACEA (version 1.0.1)

score_drugs_RWR_based: RWR-based Scoring of Drugs

Description

RWR-based Scoring of Drugs

Usage

score_drugs_RWR_based(
  driveR_res,
  drug_interactions_df,
  W_mat,
  alpha = 0.05,
  max.iter = 1000,
  eps = 1e-04,
  drug_name_col = "drug_name",
  target_col = "gene_name",
  verbose = TRUE
)

Value

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

Arguments

driveR_res

data frame of driveR results

drug_interactions_df

data frame of drug-gene interactions

W_mat

adjacency matrix for the PIN

alpha

restart parameter, controlling trade-off between prior information and network smoothing

max.iter

maximum allowed number of iterations (default = 1000)

eps

epsilon value to assess the L2 norm of the difference between iterations (default = 1e-4)

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)

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_RWR_based(
  driveR_res = toy_data,
  drug_interactions_df = toy_interactions,
  W_mat = toy_W_mat, verbose = FALSE
)