BiocSingularParam {BiocSingular} | R Documentation

## BiocSingularParam classes

### Description

Classes for specifying the type of singular value decomposition (SVD) algorithm and associated parameters.

### Usage

    ExactParam(deferred=FALSE, fold=Inf)

    IrlbaParam(deferred=FALSE, fold=Inf, extra.work=7, ...)

    RandomParam(deferred=FALSE, fold=Inf, ...)

    bsfold(object)

    bsdeferred(object)

### Arguments

`deferred` | Logical scalar indicating whether centering/scaling should be deferred, see `?"BiocSingular-options"`.
`fold` | Numeric scalar specifying the minimum fold-difference for cross-product calculation, see `?"BiocSingular-options"`.
`extra.work` | Integer scalar, additional dimensionality of the workspace in `runIrlbaSVD`.
`...` | Additional arguments to pass to `runIrlbaSVD` or `runRandomSVD`.
`object` | A BiocSingularParam object.

### Details

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.

### Value

The constructors return a BiocSingularParam subclass of the same type, containing the specified parameters.

### Methods

`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.

### Author(s)

Aaron Lun

### See Also

`runSVD` for generic dispatch.

`runExactSVD`, `runIrlbaSVD` and `runRandomSVD` for specific methods.

### Examples

    ExactParam()

    IrlbaParam(tol=1e-8)

    RandomParam(q=20)

[Package BiocSingular version 1.0.0 Index]