From c0435448051f02373e2fdeee270f4d814c526b3e Mon Sep 17 00:00:00 2001 From: jotsetung Date: Tue, 17 Oct 2017 11:07:30 +0200 Subject: [PATCH] Add note explaining precursorScanNum being set to 0 --- R/methods-write.R | 8 ++++---- man/writeMSData.Rd | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/R/methods-write.R b/R/methods-write.R index cdf9c8a6e..bbfdc478b 100644 --- a/R/methods-write.R +++ b/R/methods-write.R @@ -25,10 +25,10 @@ #' m/z or base peak intensity are calculated from the actual spectrum data #' before writing the data to the files. #' -#' For MSn data, if the `OnDiskMSnExp` or `MSnExp` does not contain also the -#' precursor scan of a MS level > 1 spectrum `precursorMZ`, -#' `precursorCharge` and `precursorIntensity` of the spectrum is set to 0 -#' in the output file. +#' For MSn data, if the `OnDiskMSnExp` or `MSnExp` does not contain also +#' the precursor scan of a MS level > 1 spectrum (e.g. due to filtering on +#' the MS level) `precursorScanNum` is set to 0 in the output file to +#' avoid potentially linking to a wrong spectrum. #' #' @param object `OnDiskMSnExp` or `MSnExp` object. #' diff --git a/man/writeMSData.Rd b/man/writeMSData.Rd index eb53ae73f..159ad057d 100644 --- a/man/writeMSData.Rd +++ b/man/writeMSData.Rd @@ -56,10 +56,10 @@ mzML file. \note{ General spectrum data such as total ion current, peak count, base peak m/z or base peak intensity are calculated from the actual spectrum data -before writing the data to the files.\preformatted{For MSn data, if the `OnDiskMSnExp` or `MSnExp` does not contain also the -precursor scan of a MS level > 1 spectrum `precursorMZ`, -`precursorCharge` and `precursorIntensity` of the spectrum is set to 0 -in the output file. +before writing the data to the files.\preformatted{For MSn data, if the `OnDiskMSnExp` or `MSnExp` does not contain also +the precursor scan of a MS level > 1 spectrum (e.g. due to filtering on +the MS level) `precursorScanNum` is set to 0 in the output file to +avoid potentially linking to a wrong spectrum. } } \author{