msmsWorkflow {RMassBank} | R Documentation |
Extracts and processes spectra from a specified file list, according to loaded options and given parameters.
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)
w |
A |
mode |
|
steps |
Which steps of the workflow to process. See the vignette
|
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 ( |
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
|
analyzeMethod |
The "method" parameter to pass to |
progressbar |
The progress bar callback to use. Only needed for specialized applications.
Cf. the documentation of |
MSe |
A boolean value that determines whether the spectra were recorded using MSe or not |
The filenames of the raw LC-MS runs are read from the array files
in the global enviroment.
See the vignette vignette("RMassBank")
for further details about the
workflow.
The processed msmsWorkspace
.
Michael Stravs, Eawag <michael.stravs@eawag.ch>