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 <[e-mail]>

See Also

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

Examples

showClass("MSnProcess")

lgatto/MSnbase documentation built on March 14, 2024, 7:06 a.m.