R/clean_ProteomeDiscoverer.R

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

#' Clean raw Proteome Discoverer data
#' @inheritParams .cleanRawPDTMT
#' @inheritParams .cleanRawPDMSstats
#' @return data.table
.cleanRawPD = function(msstats_object, quantification_column, protein_id_column,
                       sequence_column, remove_shared, 
                       remove_protein_groups = TRUE,
                       intensity_columns_regexp = "Abundance") {
  if (getDataType(msstats_object) == "MSstatsTMT") {
    cleaned_pd = .cleanRawPDTMT(msstats_object, remove_shared,
                                remove_protein_groups, 
                                protein_id_column, intensity_columns_regexp)
  } else {
    cleaned_pd = .cleanRawPDMSstats(msstats_object, quantification_column, 
                                    protein_id_column, sequence_column, 
                                    remove_shared)
  }
  .logSuccess("ProteomeDiscoverer", "clean")
  cleaned_pd
}

#' Clean raw PD output
#' @param msstats_object an object of class `MSstatsSpectroMineFiles`.
#' @param quantification_column chr, name of a column used for quantification.
#' @param protein_id_column chr, name of a column with protein IDs.
#' @param sequence_column chr, name of a column with peptide sequences.
#' @param remove_shared lgl, if TRUE, shared peptides will be removed.
#' @return data.table
#' @keywords internal
.cleanRawPDMSstats = function(msstats_object, quantification_column, 
                              protein_id_column, sequence_column, remove_shared
) {
  XProteins = NULL
  
  pd_input = getInputFile(msstats_object, "input")
  protein_id_column = .standardizeColnames(protein_id_column)
  sequence_column = .standardizeColnames(sequence_column)
  quantification_column = .standardizeColnames(quantification_column)
  
  if (remove_shared & is.element("XProteins", colnames(pd_input))) {
    pd_input = pd_input[XProteins == "1", ]
  }
  pd_cols = c(protein_id_column, sequence_column, 
              "Modifications", "Charge", "SpectrumFile", quantification_column)
  if (any(is.element(colnames(pd_input), "Fraction"))) {
    pd_cols = c(pd_cols, "Fraction")
  }
  pd_input = pd_input[, pd_cols, with = FALSE]
  data.table::setnames(
    pd_input,
    c(protein_id_column, sequence_column, "SpectrumFile", 
      quantification_column, "Charge"),
    c("ProteinName", "PeptideSequence", "Run", 
      "Intensity", "PrecursorCharge"),
    skip_absent = TRUE)
  pd_input[["PeptideSequence"]] = paste(pd_input[["PeptideSequence"]], 
                                        pd_input[["Modifications"]], 
                                        sep = "_")
  pd_input[, !(colnames(pd_input) == "Modifications"), with = FALSE]
}


#' Clean raw TMT data from Proteome Discoverer
#' @inheritParams .cleanRawPDMSstats
#' @param remove_protein_groups if TRUE, proteins with numProteins > 1 will be removed.
#' @param intensity_columns_regexp regular expressions that defines intensity columns.
#' Defaults to "Abundance", which means that columns that contain the word "Abundance"
#' will be treated as corresponding to intensities for different channels.
#' @importFrom data.table melt
#' @return `data.table`
#' @keywords internal
.cleanRawPDTMT = function(msstats_object, remove_shared = TRUE, 
                          remove_protein_groups = TRUE,
                          protein_id_column = "ProteinAccessions",
                          intensity_columns_regexp = "Abundance") {
  ProteinName = numProtein = QuanInfo = NULL
  
  pd_input = getInputFile(msstats_object, "input")
  protein_id_column = .standardizeColnames(protein_id_column)
  if (!is.element(protein_id_column, colnames(pd_input))) {
    protein_id_column = .findAvailable(c("ProteinAccessions", 
                                         "MasterProteinAccessions"),
                                       colnames(pd_input), 
                                       "ProteinAccessions")
  }
  if (protein_id_column == "ProteinAccessions") {
    num_proteins = .findAvailable(c("XProteins", 
                                    "NumberofProteins"),
                                  colnames(pd_input), 
                                  "XProteins")
  } else {
    num_proteins = .findAvailable(c("XProteinGroups", 
                                    "NumberofProteinGroups"),
                                  colnames(pd_input), 
                                  "XProteinGroups")
  }
  
  channels = .getChannelColumns(colnames(pd_input), intensity_columns_regexp)
  .validatePDTMTInputColumns(pd_input, protein_id_column, num_proteins, channels)
  
  pd_cols = intersect(c(protein_id_column, num_proteins, "AnnotatedSequence", 
                        "Charge", "PrecursorCharge", "IonsScore", 
                        "SpectrumFile", "QuanInfo", 
                        "IsolationInterference", channels),
                      colnames(pd_input))
  pd_input = pd_input[, pd_cols, with = FALSE]
  data.table::setnames(pd_input,
                       c(protein_id_column, num_proteins, "AnnotatedSequence", 
                         "SpectrumFile", "Charge"),
                       c("ProteinName", "numProtein", "PeptideSequence", 
                         "Run", "PrecursorCharge"),
                       skip_absent = TRUE)
  pd_input = unique(pd_input)
  pd_input$PSM = paste(pd_input$PeptideSequence, pd_input$PrecursorCharge,
                       1:nrow(pd_input), sep = "_")
  pd_input = melt(pd_input, measure.vars = channels, 
                  id.vars = setdiff(colnames(pd_input), channels),
                  variable.name = "Channel", value.name = "Intensity")
  pd_input$Channel = .standardizeColnames(pd_input$Channel)
  pd_input$Channel = gsub(intensity_columns_regexp, "", pd_input$Channel)
  pd_input$Channel = gsub(":", "", pd_input$Channel)
  pd_input$Intensity = ifelse(pd_input$Intensity == 0, NA, pd_input$Intensity)
  pd_input = pd_input[(ProteinName != "") & (!is.na(ProteinName)), ]
  if (remove_protein_groups) {
    pd_input = pd_input[numProtein == 1]
  }
  if (remove_shared) {
    if ("UNIQUE" %in% toupper(pd_input[["QuanInfo"]])) {
      pd_input = pd_input[toupper(QuanInfo) == 'UNIQUE', ]
    }
  }
  pd_input
}


#' Helper method to validate input has necessary columns
#' @param pd_input data.frame input
#' @param protein_id_column column name for protein passed from user
#' @param num_proteins_column column name for number of protein groups passed from user
#' @param channels list of column names for channels
.validatePDTMTInputColumns = function(pd_input, 
                                protein_id_column, 
                                num_proteins_column, 
                                channels
) {
    required_columns = c(protein_id_column, num_proteins_column, "AnnotatedSequence", 
      "SpectrumFile")
    missing_columns = setdiff(required_columns, colnames(pd_input))
    if (length(missing_columns) > 0) {
        msg = paste("The following columns are missing from the input data:", 
                    paste(missing_columns, sep = ", ", collapse = ", "))
        getOption("MSstatsLog")("ERROR", msg)
        stop(msg)
    }
    if (length(channels) == 0L) {
        msg = paste("There is no channel intensity column in the input data,",
                    "which should start with the string provided in the",
                    "intensity_columns_regexp parameter (default: 'Abundance')")
        getOption("MSstatsLog")("ERROR", msg)
        stop(msg)
    }
}