R/cleanMITAB25.R

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

##' \code{cleanMITAB} extracts and cleans a set of columns of MITAB2.5
##' @description function called internally by \code{\link{cleanMITAB}} if the format is MITAB2.5. No column names.
##' @param mitab data.table containing molecular interaction data in MITAB 2.5 format
##' @author Vitalii Kleshchevnikov
##' @import data.table
cleanMITAB25 = function(mitab){

  # if columns have no names
  if(mean(colnames(mitab) %in% paste0("V", seq_len(15))) == 1){

    # cleaning Taxid "taxid:9606(human)|taxid:9606(Homo sapiens)" to 9606
    mitab[, Taxid_interactor_A := gsub("taxid:|\\(.*$","",V10)]
    mitab[, Taxid_interactor_B := gsub("taxid:|\\(.*$","",V11)]
    # saving identifier types and cleaning interactor ids
    mitab[, interactor_IDs_databases_A := gsub(":.*$","",V1)]
    mitab[, interactor_IDs_databases_B := gsub(":.*$","",V2)]
    mitab[, IDs_interactor_A := gsub("^.*:","",V1)]
    mitab[, IDs_interactor_B := gsub("^.*:","",V2)]
    # isoform "-1" is a canonical sequence, IntAct uses isoform "-1" when it's clear that the isoform is "-1" and a canonical identifier if it's not clear which isoform was used in the experiment. Removing isoform sign "-1":
    mitab[, IDs_interactor_A := gsub("-1$", "", IDs_interactor_A)]
    mitab[, IDs_interactor_B := gsub("-1$", "", IDs_interactor_B)]
    # cleaning other information
    mitab[, Publication_Identifiers := gsub("^.*pubmed:|\\|.*$","",V9)]
    mitab[, Confidence_values := gsub(".*intact-miscore:","",V15)]

  } else {
    # rename columns to be data.table compatible
    colnames(mitab) = gsub(" ", "_", colnames(mitab))
    colnames(mitab) = gsub("\\(|\\)", "", colnames(mitab))
    colnames(mitab) = gsub("#", "", colnames(mitab))

    # cleaning Taxid "taxid:9606(human)|taxid:9606(Homo sapiens)" to 9606
    mitab[, Taxid_interactor_A := gsub("taxid:|\\(.*$","",Taxid_interactor_A)]
    mitab[, Taxid_interactor_B := gsub("taxid:|\\(.*$","",Taxid_interactor_B)]
    # saving identifier types and cleaning interactor ids
    mitab[, interactor_IDs_databases_A := gsub(":.*$","",IDs_interactor_A)]
    mitab[, interactor_IDs_databases_B := gsub(":.*$","",IDs_interactor_B)]
    mitab[, IDs_interactor_A := gsub("^.*:","",IDs_interactor_A)]
    mitab[, IDs_interactor_B := gsub("^.*:","",IDs_interactor_B)]
    # isoform "-1" is a canonical sequence, IntAct uses isoform "-1" when it's clear that the isoform is "-1" and a canonical identifier if it's not clear which isoform was used in the experiment. Removing isoform sign "-1":
    mitab[, IDs_interactor_A := gsub("-1$", "", IDs_interactor_A)]
    mitab[, IDs_interactor_B := gsub("-1$", "", IDs_interactor_B)]
    # cleaning other information
    mitab[, Publication_Identifiers := gsub("^.*pubmed:|\\|.*$","",Publication_Identifiers)]
    mitab[, Confidence_values := gsub(".*intact-miscore:","",Confidence_values)]
  }
  mitab[, Confidence_values := gsub("-","NA",Confidence_values)]
  # supress expected warning (NA introduced by coersion to numeric) to avoid confusion
  suppressWarnings({mitab[, Confidence_values := as.numeric(Confidence_values)]})
  #mitab[, Interaction_identifiers := unlist(gsubfn::strapplyc(Interaction_identifiers,"EBI-[[:digit:]]+",simplify = T)), by =Interaction_identifiers]
  # generating unique identifier for interacting pairs
  mitab[, pair_id := {
    z = sort(c(IDs_interactor_A, IDs_interactor_B))
    paste0(z[1],"|",z[2])
  }, by = .(IDs_interactor_A,IDs_interactor_B)]

  # reorder by all interactor attribute columns by pair_id (alphanumeric order)
  mitab[, c("IDs_A_order", "IDs_B_order") := tstrsplit(pair_id, "\\|")]
  mitab = reorderMITAB25(mitab)

  return(mitab)
}

##' \code{reorderMITAB25} reorders interacting molecules in a pair (and all the corresponding columns) according to order provided in IDs_A_order and IDs_B_order columns (latter are deleted)
##' @name reorderMITAB25
##' @description function called internally by \code{\link{cleanMITAB25}} if the format is MITAB2.5
##' @param mitab data.table containing molecular interaction data in MITAB 2.5 format
##' @author Vitalii Kleshchevnikov
##' @import data.table
reorderMITAB25 = function(mitab){
  if(mean(c("IDs_A_order", "IDs_B_order") %in% colnames(mitab)) != 1) stop("columns to order by not provided (IDs_A_order, IDs_B_order)") else {
    mitab[IDs_interactor_A == IDs_B_order & IDs_interactor_B == IDs_A_order,
          c("IDs_interactor_A", "IDs_interactor_B",
            "interactor_IDs_databases_A", "interactor_IDs_databases_B",
            "Taxid_interactor_A", "Taxid_interactor_B") :=
            .(IDs_interactor_B, IDs_interactor_A,
              interactor_IDs_databases_B, interactor_IDs_databases_A,
              Taxid_interactor_B, Taxid_interactor_A)]

    mitab = unique(mitab[,.(IDs_interactor_A, IDs_interactor_B,
                            interactor_IDs_databases_A, interactor_IDs_databases_B,
                            Taxid_interactor_A, Taxid_interactor_B,
                            Publication_Identifiers, Confidence_values,
                            pair_id)])
    return(mitab)
  }
}