R/measure_distances.R

In nogay/drugdealR: Suggest Drug Combination Options for Comorbid Patients

#' Check if distance matrix of a disease changes after removing a given drug
#'
#' @param disease name of the disease of interest (compatible with DisNor).
#' @param drug name of the drug of interest (compatible with Drugbank).
#' @param gr the interactome igraph graph object.
#'
#' @return logical
#' @export
#'
#' @examples
#' \dontrun{
#' library(drugdealR)
#' measure_dists('Myeloid Leukemia, Chronic', 'Imatinib', gr)
#' }

measure_dists <- function(disease, drug, interactome_gr, interactome_df){
  gr_noDrug <- interactome_df[-which(interactome_df$Protein_A == drug),]
  gr_noDrug <- igraph::graph_from_data_frame(gr_noDrug)
  gr_noDrug <- igraph::as.undirected(gr_noDrug)
  gr_noDrug <- igraph::simplify(gr_noDrug, remove.multiple = TRUE, remove.loops = TRUE)
  disNetDists <- sapply(disease, function(x) igraph::distances(interactome_gr,v=x,to=disease))
  disNetDists <- as.numeric(disNetDists)
  disNetDists_noDrug <- sapply(disease, function(x) igraph::distances(gr_noDrug,v=x,to=disease))
  rownames(disNetDists_noDrug) <- disease
  disNetDists_noDrug <- as.numeric(disNetDists_noDrug)
  return(all.equal(disNetDists,disNetDists_noDrug))
}