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
.
MSnbaseOptions()
isMSnbaseVerbose()
setMSnbaseVerbose(opt)
setMSnbaseParallelThresh(opt = 1000)
setMSnbaseFastLoad(opt = TRUE)
isMSnbaseFastLoad()
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.