MSnProcess-class {MSnbase} | R Documentation

## The "MSnProcess" Class

### Description

`MSnProcess` is a container for MSnExp and MSnSet processing information. It records data files, processing steps, thresholds, analysis methods and times that have been applied to MSnExp or MSnSet instances.

### Slots

`files`:

  Object of class `"character"` storing the raw data files used in experiment described by the `"MSnProcess"` instance.

`processing`:

  Object of class `"character"` storing all the processing steps and times.

`merged`:

  Object of class `"logical"` indicating whether spectra have been merged.

`cleaned`:

  Object of class `"logical"` indicating whether spectra have been cleaned. See `clean` for more details and examples.

`removedPeaks`:

  Object of class `"character"` describing whether peaks have been removed and which threshold was used. See `removePeaks` for more details and examples.

`smoothed`:

  Object of class `"logical"` indicating whether spectra have been smoothed.

`trimmed`:

  Object of class `"numeric"` documenting if/how the data has been trimmed.

`normalised`:

  Object of class `"logical"` describing whether and how data have been normalised.

`MSnbaseVersion`:

  Object of class `"character"` indicating the version of MSnbase.

`.__classVersion__`:

  Object of class `"Versions"` indicating the version of the `MSnProcess` instance. Intended for developer use and debugging.

### Extends

Class `"Versioned"`, directly.

### Methods

fileNames

  `signature(object = "MSnProcess")`: Returns the file names used in experiment described by the `"MSnProcess"` instance.

show

  `signature(object = "MSnProcess")`: Displays object content as text.

combine

  `signature(x = "MSnProcess", y = "MSnProcess")`: Combines multiple `MSnProcess` instances.

### Note

This class is likely to be updated using an `AnnotatedDataFrame`.

### Author(s)

Laurent Gatto <lg390@cam.ac.uk>

### See Also

See the `"MSnExp"` and `"MSnSet"` classes that actually use `MSnProcess` as a slot.

### Examples

    showClass("MSnProcess")

[Package MSnbase version 2.20.1 Index]