R/edgelist2degreeFreq.R

In vitkl/MItools: Protein interaction data tools: retrieving data from IntAct and most other databases using PSICQUIC service

##' Find the degree distribution given edgelist (pair_id) and a list of proteins which degrees matter
##' @name edgelist2degreeFreq
##' @author Vitalii Kleshchevnikov
##' @details unique pair_id is the unique identifier of the undirected interaction: ordered alphabetically and concatenated interacting molecule IDs \code{\link{cleanMITAB}}
##' @param mitab data.table containing molecular interaction data, including pair_id
##' @param prots list of relevant proteins, degree distribution is based on the prevalence of specific degrees in this list, all proteins in \code{mitab} by default
##' @param sep ID separator in pair_id, passed to \code{\link{edgelist2degree}}
##' @import data.table
##' @export edgelist2degreeFreq
##' @examples
##' if(F) {
##' # download full human interactome (clean = TRUE is necessary to produce the right input for edgelist2degree)
##' full = fullInteractome(taxid = "9606", database = "IntActFTP", format = "tab25", clean = TRUE, protein_only = TRUE)
##' degree_freq = edgelist2degreeFreq(full)
##' plot(degree_freq$N, degree_freq$degree_freq,
##'      log = "xy",
##'      main = "degree distribution \n - human-human protein interactions -",
##'      ylab = "degree frequency, log-scale",
##'      xlab = "degree, log-scale",
##'      las=1)
##' }
edgelist2degreeFreq = function(mitab, prots = NULL){
  if(!(is.data.table(mitab) & c("IDs_interactor_A", "IDs_interactor_B") %in% colnames(mitab))) stop("mitab table (edge list) is not data.table or doesn't contain IDs_interactor_A and IDs_interactor_B columns")
  # use all proteins in mitab if no protein list supplied
  if(is.null(prots)) prots = mitab[, unique(c(IDs_interactor_A, IDs_interactor_B))]

  mitab = copy(mitab)
  # compute degree
  degree = edgelist2degree(mitab)[ID %in% prots,]
  # compute degree count
  degree_dist = unique(degree[, count := .N, by = N][, .(N,count)])
  # compute degree frequency
  degree_dist[, degree_freq := count / sum(count)]
  return(degree_dist[,.(N, degree_freq)])
}