msmsRead.RAW: Extracts and processes spectra from a list of xcms-Objects

In sneumann/RMassBank: Workflow to process tandem MS files and build MassBank records

Description

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.

Usage

msmsRead.RAW(
  w,
  xRAW = NULL,
  cpdids = NULL,
  mode,
  findPeaksArgs = NULL,
  settings = getOption("RMassBank"),
  progressbar = "progressBarHook",
  plots = FALSE
)

Arguments

w	A msmsWorkspace to work with.
xRAW	A list of xcmsRaw objects whose peaks should be detected and added to the workspace. The relevant data must be in the MS1 data of the xcmsRaw object. You can coerce the msn-data in a usable object with the msn2xcmsRaw function of xcms.
cpdids	A vector or list containing the compound IDs of the files that are to be read as spectra. The ordering of this and files implicitly assigns each ID to the corresponding file. If this is supplied, then the IDs implicitly named in the filenames are ignored.
mode	"pH", "pNa", "pM", "pNH4", "mH", "mM", "mFA" for different ions ([M+H]+, [M+Na]+, [M]+, [M+NH4]+, [M-H]-, [M]-, [M+FA]-).
findPeaksArgs	A list of arguments that will be handed to the xcms-method findPeaks via do.call
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.
plots	A boolean value that determines whether the pseudospectra in XCMS should be plotted

Value

The msmsWorkspace with msms-spectra read.

Author(s)

Michael Stravs, Eawag <[e-mail]>

Erik Mueller, UFZ

See Also

msmsWorkspace-class, msmsWorkflow

sneumann/RMassBank documentation built on Oct. 20, 2020, 3:19 p.m.