Nothing
#' Clean raw OpenSWATH files
#' @param msstats_object an object of class `MSstatsSpectroMineFiles`.
#' @return data.table
#' @keywords internal
.cleanRawOpenSWATH = function(msstats_object) {
PeptideSequence = FragmentIon = Intensity = NULL
os_input = getInputFile(msstats_object, "input")
os_input = os_input[, c("ProteinName", "FullPeptideName", "Charge",
"filename", "aggr_Fragment_Annotation",
"aggr_Peak_Area", "m_score", "decoy"), with = FALSE]
data.table::setnames(
os_input,
c("FullPeptideName", "Charge", "filename",
"aggr_Fragment_Annotation", "aggr_Peak_Area"),
c("PeptideSequence", "PrecursorCharge", "Run",
"FragmentIon", "Intensity"),
skip_absent = TRUE)
os_input = os_input[, c("ProteinName", "PeptideSequence", "PrecursorCharge",
"Run", "FragmentIon", "Intensity",
"m_score", "decoy"), with = FALSE]
os_input$Intensity = as.character(os_input$Intensity)
os_input = os_input[
, lapply(.SD,
function(x) unlist(tstrsplit(x, split = ";", fixed = TRUE))),
by = c("ProteinName", "PeptideSequence", "PrecursorCharge",
"Run", "m_score", "decoy"),
.SDcols = c("FragmentIon", "Intensity")]
os_input[, c("PeptideSequence", "FragmentIon") := lapply(
list(PeptideSequence, FragmentIon), function(x) gsub(":", "_", x)
)]
os_input[, Intensity := as.numeric(as.character(Intensity))]
os_input[, Intensity := ifelse(Intensity < 1, NA, Intensity)]
.logSuccess("OpenSWATH", "clean")
os_input
}
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