Approximate SVD is performed using the implementation from irlba, randomized SVD is performed using the implementation from rsvd.

randomized_svd(object, exprs_values, n_dims, features = NULL,
  skip = NULL, seed = NULL, ...)

approximate_svd(object, exprs_values, n_dims, features = NULL,
  skip = NULL, seed = NULL, ...)

Arguments

object

A SingleCellExperiment object.

exprs_values

String indicating which assay contains the data that should be used to perform SVD.

n_dims

The number of approximate singular values to calculate.

features

A character vector (of feature names), a logical vector or numeric vector (of indices) specifying the features to use for SVD. The default of NULL will use all features.

skip

A numeric vector indicating which singular values to set to zero (and remove).

seed

A numeric seed to initialize the random number generator.

...

Additional arguments passed on to rsvd or irlba.

Value

A matrix of dimension ncol(object) x dims(object) - length(skip).