MSnbase: MSnbaseOptions – R documentation

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MSnbaseOptions

MSnbase options

Description

MSnbase defined a few options globally using the standard R options mechanism. The current values of these options can be queried with MSnbaseOptions. The options are:

verbose: defines a session-wide verbosity flag, that is used if the verbose argument in individual functions is not set.
PARALLEL_THRESH: defines the minimum number of spectra per file necessary before using parallel processing.
fastLoad: logical(1). If TRUE performs faster data loading for all methods of OnDiskMSnExp that load data from the original files (such as spectrapply()). Users experiencing data I/O errors (observed mostly on macOS systems) should set this option to FALSE.

Usage

MSnbaseOptions()

isMSnbaseVerbose()

setMSnbaseVerbose(opt)

setMSnbaseParallelThresh(opt = 1000)

setMSnbaseFastLoad(opt = TRUE)

isMSnbaseFastLoad()

Arguments

opt

The value of the new option

Details

isMSnbaseVerbose is one wrapper for the verbosity flag, also available through options("MSnbase")$verbose.

There are also setters to set options individually. When run without argument, the verbosity setter inverts the current value of the option.

Value

A list of MSnbase options and the single option values for the individual accessors.

MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics

v2.16.1

Artistic-2.0

Authors

Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker and Lieven Clement.

Initial release