R/clean_MaxQuant.R

In Vitek-Lab/MSstatsConvert: Import Data from Various Mass Spectrometry Signal Processing Tools to MSstats Format

#' Clean raw output from MaxQuant
#' @param msstats_object object that inherits from MSstatsInputFiles class.
#' @param protein_id_col character, name of a column with names of proteins.
#' @param remove_by_site logical, if TRUE, proteins only identified by site will
#' be removed.
#' @param channel_columns character, regular expression that identifies channel columns
#' in TMT data.
#' @return data.table
#' @keywords internal
.cleanRawMaxQuant = function(msstats_object, protein_id_col, 
                             remove_by_site = FALSE,
                             channel_columns = "Reporterintensitycorrected"
) {
  ProteinIDs = id = PSM = PeptideSequence = NULL
  ProteingroupIDs = PrecursorCharge = Intensity = NULL
  
  mq_input = getInputFile(msstats_object, "evidence")
  mq_pg = getInputFile(msstats_object, "protein_groups")
  
  filter_cols = c("Contaminant", "Potentialcontaminant", "Reverse")
  msg = paste("** + Contaminant, + Reverse, + Potential.contaminant",
              "proteins are removed.")
  if (remove_by_site) {
    filter_cols = c(filter_cols, "Onlyidentifiedbysite")
    msg = paste("** + Contaminant, + Reverse, + Potential.contaminant,", 
                "+ Only.identified.by.site proteins are removed.")
  }
  
  mq_input = .filterManyColumns(mq_input, filter_cols, "+")
  mq_pg = .filterManyColumns(mq_pg, filter_cols, "+")
  getOption("MSstatsLog")("INFO", msg)
  getOption("MSstatsMsg")("INFO", msg)
  
  suppressWarnings({
    mq_input[, ProteingroupIDs := as.integer(as.character(ProteingroupIDs))]
  })
  
  if (getDataType(msstats_object) == "MSstats") {
    mq_input = mq_input[ProteingroupIDs %in% unique(mq_pg[["id"]]), ]
  }
  
  mq_input = merge(mq_input, 
                   unique(mq_pg[, list(uniquefromProteinGroups = ProteinIDs,
                                       ProteingroupIDs = id)]),
                   by = "ProteingroupIDs", sort = FALSE)
  
  if (getDataType(msstats_object) == "MSstatsTMT") {
    protein_id = .findAvailable(c("Proteins", "Leadingproteins", 
                                  "Leadingrazorprotein", "Genenames"),
                                protein_id_col, "Proteins")
    channels = .getChannelColumns(colnames(mq_input), channel_columns)
  } else {
    protein_id = ifelse(protein_id_col == "Proteins", 
                        "uniquefromProteinGroups",
                        "Leadingrazorprotein")
    channels = character(0)
  }
  data.table::setnames(
    mq_input, 
    c(protein_id, "Modifiedsequence", "Charge", "Rawfile"), 
    c("ProteinName", "PeptideSequence", "PrecursorCharge", "Run"),
    skip_absent = TRUE)
  mq_input[["PeptideSequence"]] = gsub("_", "", mq_input[["PeptideSequence"]])
  mq_cols = c("ProteinName", "PeptideSequence", "Modifications", 
              "PrecursorCharge", "Run", "Intensity", 
              "Fraction", "TechReplicate", "Run", "BioReplicate",
              "PSM", "Score")
  mq_cols = intersect(c(mq_cols, channels),
                      colnames(mq_input))
  mq_input = mq_input[, mq_cols, with = FALSE]
  mq_input = unique(mq_input)
  
  if (getDataType(msstats_object) == "MSstatsTMT") {
    mq_input[, PSM := paste(PeptideSequence, PrecursorCharge, 
                            1:nrow(mq_input), sep = "_")]
    mq_input = melt(mq_input, measure.vars = channels,
                    id.vars = c("ProteinName", "PeptideSequence", 
                                "PrecursorCharge", "PSM", "Run", "Score"),
                    variable.name = "Channel", value.name = "Intensity")
    mq_input$Channel = gsub(channel_columns, "channel", mq_input$Channel)
    mq_input$Channel = .standardizeColnames(mq_input$Channel)
    suppressWarnings({
      mq_input$Intensity = ifelse(mq_input$Intensity == 0, NA,
                                  mq_input$Intensity)
    })
    mq_input = .filterFewMeasurements(mq_input, 0, FALSE, 
                                      c("PeptideSequence", 
                                        "PrecursorCharge", "Run"))
  }
  
  mq_input = mq_input[!is.na(Intensity), ]
  .logSuccess("MaxQuant", "clean")
  mq_input
}