Usage
msmsWorkflow(w, mode = "pH", steps = c(1:8), confirmMode = FALSE, newRecalibration = TRUE, useRtLimit = TRUE, archivename = NA, readMethod = "mzR", findPeaksArgs = NULL, plots = FALSE, precursorscan.cf = FALSE, settings = getOption("RMassBank"), analyzeMethod = "formula", progressbar = "progressBarHook", MSe = FALSE)
Arguments
w
A msmsWorkspace to work with.
mode
"pH", "pNa", "pM", "mH", "mM", "mFA", "pNH4" for different ions
([M+H]+, [M+Na]+, [M]+, [M-H]-, [M]-, [M+FA]-, [M+NH4]+).
steps
Which steps of the workflow to process. See the vignette
vignette("RMassBank") for details.
confirmMode
Defaults to false (use most intense precursor). Value 1 uses
the 2nd-most intense precursor for a chosen ion (and its data-dependent scans)
, etc.
newRecalibration
Whether to generate a new recalibration curve (TRUE, default) or
to reuse the currently stored curve (FALSE, useful e.g. for adduct-processing runs.)
useRtLimit
Whether to enforce the given retention time window.
archivename
The prefix under which to store the analyzed result files.
readMethod
Several methods are available to get peak lists from the files.
Currently supported are "mzR", "xcms", "MassBank" and "peaklist".
The first two read MS/MS raw data, and differ in the strategy
used to extract peaks. MassBank will read existing records,
so that e.g. a recalibration can be performed, and "peaklist"
just requires a CSV with two columns and the column header "mz", "int".
findPeaksArgs
A list of arguments that will be handed to the xcms-method findPeaks via do.call
plots
A parameter that determines whether the spectra should be plotted or not (This parameter is only used for the xcms-method)
precursorscan.cf
Whether to fill precursor scans. To be used with files which for
some reasons do not contain precursor scan IDs in the mzML, e.g. AB Sciex converted
files.
settings
Options to be used for processing. Defaults to the options loaded via
loadRmbSettings et al. Refer to there for specific settings. progressbar
The progress bar callback to use. Only needed for specialized applications.
Cf. the documentation of progressBarHook for usage. MSe
A boolean value that determines whether the spectra were recorded using MSe or not