MSnProcess-class: The "MSnProcess" Class

In lgatto/MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

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

See Also

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

Examples

showClass("MSnProcess")

lgatto/MSnbase documentation built on Nov. 12, 2024, 10:58 a.m.