R/utils_dt_operations.R

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

#' Read file from a provided path or convert given data.frame to data.table
#' @param input report from a signal processing tool or a path to it
#' @param ... additional parameters for data.table::fread
#' @importFrom data.table as.data.table fread
#' @return data.table
#' @keywords internal
.getDataTable = function(input, ...) {
    checkmate::checkTRUE(is.character(input) | inherits(input, "data.frame"))
    if (inherits(input, "data.frame")) {
        input = data.table::as.data.table(input)
    } else {
        input = data.table::fread(input, showProgress = FALSE, ...)
    }
    colnames(input) = .standardizeColnames(colnames(input))
    input
}


#' Remove underscores from sequences and change intensity type to numeric
#' @param input data.table
#' @return data.table
#' @keywords internal
.fixBasicColumns = function(input) {
  Intensity = PeptideSequence = FragmentIon = NULL
  
  input[, Intensity := as.numeric(Intensity)]
  input[, PeptideSequence := stringi::stri_replace_all(PeptideSequence, 
                                                       "", fixed = "_")]
  input[, FragmentIon := stringi::stri_replace_all(FragmentIon, "",
                                                   fixed = "_")]
  input
}


#' Change classes of multiple columns
#' @param input data.table preprocessed by one of the `cleanRaw*` functions.
#' @param numeric_columns chr, vector of names of columns that will be 
#' converted to numeric.
#' @param character_columns chr, vector of names of colums taht will be 
#' converted to character.
#' @param factor_columns chr, vector of names of columns that will be 
#' converted to factor.
#' @return data.table
#' @keywords internal
.fixColumnTypes = function(input, numeric_columns = NULL, 
                           character_columns = NULL,
                           factor_columns = NULL) {
    for (column in factor_columns) {
        input[[column]] = factor(input[[column]])
    }
    for (column in numeric_columns) {
        input[[column]] = as.numeric(as.character(input[[column]]))
    }
    for (column in character_columns) {
        input[[column]] = as.character(input[[column]])
    }
    input
}


#' Set column to a single value
#' @param input data.table preprocessed by one of the `cleanRaw*` functions.
#' @param fill_list named list, names correspond to column names, elements 
#' to values that will be used in the columns.
#' @return data.table
#' @keywords internal
.fillValues = function(input, fill_list) {
    if (length(fill_list) > 0) {
        input[, names(fill_list) := as.list(unname(fill_list))]
    }
}


#' Change column names to match read.table/read.csv/read.delim conventions
#' @param col_names chr, vector of column names
#' @return character vector
#' @keywords internal
.standardizeColnames = function(col_names) {
    col_names = stringi::stri_replace_all(col_names, fixed = " ", replacement = ".")
    col_names = stringi::stri_replace_all(col_names, regex = "\\[|\\]|\\%", replacement = ".")
    col_names = stringi::stri_replace_all(col_names, fixed = "/", replacement = "")
    col_names = stringi::stri_replace_all(col_names, fixed = "+", replacement = "")
    col_names = stringi::stri_replace_all(col_names, fixed = "#", replacement = "X.")
    stringi::stri_replace_all(col_names, regex = "[\\.]+", replacement = "")
}


#' Get intensity columns from wide-format data
#' @param col_names names of columns, where some of the columns store intensity
#' value for different channels
#' @param ... varying number of strings that define channel columns.
#' @return character vector of column names that correspond to channel intensities
#' @keywords internal
.getChannelColumns = function(col_names, ...) {
    all_patterns = unlist(list(...))
    channel_filter = rep(TRUE, length(col_names))
    for (pattern in all_patterns) {
        channel_filter = channel_filter & grepl(pattern, col_names, 
                                                fixed = TRUE)
    }
    col_names[channel_filter]
}


#' Select columns for MSstats format
#' @param input data.table
#' @return data.table
#' @keywords internal
.selectMSstatsColumns = function(input) {
    Condition = NULL

    standard_columns = c(
        "ProteinName", "PeptideSequence", "PeptideModifiedSequence", 
        "PrecursorCharge", "FragmentIon", "ProductCharge", "IsotopeLabelType",
        "Condition", "BioReplicate", "Run", "TechReplicate", "StandardType", 
        "Fraction", "DetectionQValue", "Intensity"
      )
    
    standard_columns_tmt = c("ProteinName", "PeptideSequence", "PrecursorCharge", 
                             "PSM", "Mixture", "TechRepMixture", "Run", 
                             "Channel", "BioReplicate", "Condition", "Intensity")
    
    if (is.element("Channel", colnames(input))) {
        cols = standard_columns_tmt
        character_cols = c("ProteinName", "PeptideSequence", "PrecursorCharge",
                           "PSM", "Mixture", "TechRepMixture", "Run",
                           "Channel", "BioReplicate")
        input[, c("ProteinName", "PeptideSequence", "PrecursorCharge",
                  "PSM", "Mixture", "TechRepMixture", "Run",
                  "Channel", "BioReplicate") := lapply(.SD, as.character),
              .SDcols = character_cols]
        input[, Condition := factor(as.character(Condition))]
    } else {
        cols = standard_columns
    }
    input[, intersect(cols, colnames(input)), with = FALSE]
}