Description Usage Arguments Details General options Algorithms Parallel computations Plotting Examples
NMF Package Specific Options
1 2 3 4 5 6 7 | nmf.options(...)
nmf.getOption(x, default = NULL)
nmf.resetOptions(..., ALL = FALSE)
nmf.printOptions()
|
... |
option specifications. For For |
x |
a character string holding an option name. |
default |
if the specified option is not set in the options list, this value is returned. This facilitates retrieving an option and checking whether it is set and setting it separately if not. |
ALL |
logical that indicates if options that are not part of the default set of options should be removed. Note that in pkgmaker <= 0.9 this argument is only taken into account when no other argument is present. This is fixed in version 0.9.1. |
nmf.options
sets/get single or multiple options, that are specific
to the NMF package.
It behaves in the same way as options
.
nmf.getOption
returns the value of a single option, that is specific
to the NMF package.
It behaves in the same way as getOption
.
nmf.resetOptions
reset all NMF specific options to their default values.
nmf.printOptions
prints all NMF specific options along with their default values,
in a relatively compact way.
Interval/frequency (in number of runs) at which garbage collection is performed.
Default level of verbosity.
Toogles debug mode. In this mode the console output may be very – very – messy, and is aimed at debugging only.
% end description
Default NMF algorithm used by the nmf
function when argument
method
is missing.
The value should the key of one of the registered NMF algorithms or a valid specification of an NMF algorithm.
See ?nmfAlgorithm
.
Default seeding method used by the nmf
function when argument seed
is missing.
The value should the key of one of the registered seeding methods or a vallid specification of a seeding method.
See ?nmfSeed
.
Default maximum number of iteration to use (default NULL). This option is for internal/technical usage only, to globally speed up examples or tests of NMF algorithms. To be used with care at one's own risk... It is documented here so that advanced users are aware of its existence, and can avoid possible conflict with their own custom options.
Toggle default residual tracking.
When TRUE
, the nmf
function compute and store the residual track in the result – if not otherwise specified in argument .options
.
Note that tracking may significantly slow down the computations.
Number of iterations between two points in the residual track.
This option is relevant only when residual tracking is enabled.
See ?nmf
.
this is a symbolic link to option track
for backward compatibility.
% end description
Default number of cores to use to perform parallel NMF computations.
Note that this option is effectively used only if the global option 'cores'
is
not set.
Moreover, the number of cores can also be set at runtime, in the call to nmf
,
via arguments .pbackend
or .options
(see nmf
for more details).
Default loop/parallel foreach backend used by the nmf
function when
argument .pbackend
is missing.
Currently the following values are supported: 'par'
for multicore,
'seq'
for sequential, NA
for standard sapply
(i.e. do not use a foreach loop),
NULL
for using the currently registered foreach backend.
this is a symbolic link to option pbackend
for backward compatibility.
% end description
logical that indicates if annotated heatmaps should use a set of functions
from the grid
packages that were patched to enable mixing (TRUE
) or stock grid
functions
(FALSE
).
The default value for this option is NULL
, which avoids the saving of heatmaps in pdf files
to generate a blank first page
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | # show all NMF specific options
nmf.printOptions()
# get some options
nmf.getOption('verbose')
nmf.getOption('pbackend')
# set new values
nmf.options(verbose=TRUE)
nmf.options(pbackend='mc', default.algorithm='lee')
nmf.printOptions()
# reset to default
nmf.resetOptions()
nmf.printOptions()
|
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