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Added support for different column names in SpectroMine #99

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Added support for different column names in SpectroMine #99

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4 changes: 3 additions & 1 deletion R/clean_SpectroMine.R
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#' Clean raw SpectroMine TMT data
#' @param msstats_object an object of class `MSstatsSpectroMineFiles`.
#' @importFrom data.table melt
#' @importFrom data.table melt setnames
#' @return `data.table`
#' @keywords internal
.cleanRawSpectroMineTMT = function(msstats_object) {
Expand All @@ -14,6 +14,8 @@
getOption("MSstatsMsg")("ERROR", msg)
stop(msg)
}
pg_qval_column = grep("pgqvalue", colnames(sm_input), ignore.case = TRUE, value = TRUE)
data.table::setnames(sm_input, pg_qval_column, "PGQValue")
sm_input = sm_input[, c("PGProteinAccessions", "PMoleculeID", "PPCharge",
"PGQValue", "PSMQvalue", "RFileName", channels),
with = FALSE]
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