R/subset_graph.R

In taylorpourtaheri/nr: Node prioritization optimizer

#' @title Subset the loaded igraph based on edge confidence
#' @description Given an iGraph object from StringDb, reduce the
#' full graph to a subset based on edge confidence scores. This
#' function will improve the performance of multiple calls to
#' the iGraph object for the parameter optimization.
#' @param graph Graph of class '\code{igraph}'
#' @param score_threshold Integer value of the edge confidence'
#' @export

subset_graph <- function(graph, score_threshold){

    # add if/else here to catch error if no scores are less than threshold?

    indices <- which(igraph::E(graph)$combined_score >= score_threshold)
    # sub_ppi <- igraph::subgraph.edges(graph, igraph::E(graph)[igraph::E(graph)$combined_score >= score_threshold], del=F)
    sub_ppi <- igraph::subgraph.edges(graph, eids = igraph::E(graph)[indices], del=F)
    # sub_ppi <- connected_subgraph(sub_ppi)

  return(sub_ppi)
}