R/transform_MSstats_OpenSWATH.R

In SWATH2stats: Transform and Filter SWATH Data for Statistical Packages

#'  Transforms column names to OpenSWATH column names
#'
#' This functions transforms the column names from a data frame in MSstats
#' format to a data frame with column names used by the OpenSWATH output. The
#' original table needs to contain at least the 10 columns defined by MSstats:
#' ProteinName, PeptideSequence, PrecursorCharge, Fragmentation, ProductCharge,
#' IsotopeLabelType, Condition, BioReplicate, Run, Intensity.)
#'
#' @param data A data frame containing the SWATH data in the MSstats format
#' @return The data frame in the appropriate format.
#' @references Choi M, Chang CY, Clough T, Broudy D, Killeen T, MacLean B, Vitek
#'   O. MSstats: an R package for statistical analysis of quantitative mass
#'   spectrometry-based proteomic experiments.Bioinformatics. 2014 Sep
#'   1;30(17):2524-6. doi: 10.1093/bioinformatics/btu305.
#' @author Peter Blattmann
#' @examples
#'  data("MSstats_data", package="SWATH2stats")
#'  transformed <- transform_MSstats_OpenSWATH(MSstats_data)
#' @export
transform_MSstats_OpenSWATH <- function(data) {
    colnames(data) <- gsub("\\.", "", colnames(data))

    missing_columns <- setdiff(c("ProteinName", "PeptideSequence", "PrecursorCharge",
        "FragmentIon", "ProductCharge", "IsotopeLabelType", "Condition", "BioReplicate",
        "Run", "Intensity"), colnames(data))

    if (length(missing_columns > 0)) {
        stop(paste("The data frame doesn't contain all required columns. The following columns are missing:\n",
            paste(missing_columns, collapse = ", ")))

    }

    add.colnames <- colnames(data)[!(colnames(data) %in% c("ProteinName", "PeptideSequence",
        "PrecursorCharge", "FragmentIon", "ProductCharge", "IsotopeLabelType", "Condition",
        "BioReplicate", "Run", "Intensity"))]

    data <- data[, c("ProteinName", "PeptideSequence", "PrecursorCharge", "FragmentIon",
        "ProductCharge", "IsotopeLabelType", "Condition", "BioReplicate", "Run",
        "Intensity", add.colnames)]
    colnames(data)[seq_len(10)] <- c("ProteinName", "FullPeptideName", "Charge",
        "FragmentIon", "ProductCharge", "IsotopeLabelType", "Condition", "BioReplicate",
        "Run", "Intensity")

    if (length(add.colnames) > 0) {
        message("Additional columns present in the data: ", paste(add.colnames, collapse = ", "))
    }

    if (!("mscore" %in% colnames(data))) {
        message("No column 'mscore' present in the data. This column is required for functions estimating FDR or filtering the data.")
    }
    return(data)

}