| BiocSingularParam {BiocSingular} | R Documentation |
Classes for specifying the type of singular value decomposition (SVD) algorithm and associated parameters.
ExactParam(deferred=FALSE, fold=Inf)
IrlbaParam(deferred=FALSE, fold=Inf, extra.work=7, ...)
RandomParam(deferred=FALSE, fold=Inf, ...)
bsfold(object)
bsdeferred(object)
deferred |
Logical scalar indicating whether centering/scaling should be deferred, see |
fold |
Numeric scalar specifying the minimum fold-difference for cross-product calculation, see |
extra.work |
Integer scalar, additional dimensionality of the workspace in |
... |
Additional arguments to pass to |
object |
A BiocSingularParam object. |
The BiocSingularParam class is a virtual base class on which other parameter objects are built. There are 3 concrete subclasses:
ExactParam: exact SVD with runExactSVD.
IrlbaParam: approximate SVD with irlba via runIrlbaSVD.
RandomParam: approximate SVD with rsvd via runRandomSVD.
These objects hold parameters specifying how each algorithm should be run on an arbitrary data set. See the associated documentation pages for more details.
The constructors return a BiocSingularParam subclass of the same type, containing the specified parameters.
show(object):Display the class of a BiocSingularParam object, and a summary of the set parameters.
bsfold(object):Return a numeric scalar specifying the fold-difference for cross-product calculation.
bsdeferred(object):Return a logical scalar indicating whether centering and scaling should be deferred.
Aaron Lun
runSVD for generic dispatch.
runExactSVD, runIrlbaSVD and runRandomSVD for specific methods.
ExactParam() IrlbaParam(tol=1e-8) RandomParam(q=20)