MSnbaseOptions {MSnbase} | R Documentation

## 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.

[Package MSnbase version 2.6.4 Index]