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#' 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)
}
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