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.




setMSnbaseParallelThresh(opt = 1000)

setMSnbaseFastLoad(opt = TRUE)




The value of the new option


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


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.