msmsRead {RMassBank} | R Documentation

## Extracts and processes spectra from a specified file list, according to loaded options and given parameters.

### 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(
      w,
      filetable = NULL,
      files = NULL,
      cpdids = NULL,
      readMethod,
      mode,
      confirmMode = FALSE,
      useRtLimit = TRUE,
      Args = NULL,
      settings = getOption("RMassBank"),
      progressbar = "progressBarHook",
      MSe = FALSE,
      plots = FALSE
    )

### Arguments

`w` | A `msmsWorkspace` to work with.
`filetable` | The path to a .csv-file that contains the columns "Files" and "ID" supplying the relationships between files and compound IDs. Either this or the parameter "files" need to be specified.
`files` | A vector or list containing the filenames of the files that are to be read as spectra. For the IDs to be inferred from the filenames alone, there need to be exactly 2 underscores.
`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.
`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".
`mode` | `"pH", "pNa", "pM", "pNH4", "mH", "mM", "mFA"` for different ions ([M+H]+, [M+Na]+, [M]+, [M+NH4]+, [M-H]-, [M]-, [M+FA]-).
`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.
`useRtLimit` | Whether to enforce the given retention time window.
`Args` | 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.
`MSe` | A boolean value that determines whether the spectra were recorded using MSe or not
`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 <michael.stravs@eawag.ch>

Erik Mueller, UFZ

### See Also

`msmsWorkspace-class`, `msmsWorkflow`

[Package RMassBank version 3.0.0 Index]