Options for simple_pca(). More...

#include <simple_pca.hpp>

Public Attributes
int	number = 25

bool	scale = false

bool	transpose = true

int	num_threads = 1

bool	realize_matrix = true

irlba::Options	irlba_options

Detailed Description

Options for simple_pca().

Member Data Documentation

◆ irlba_options

irlba::Options scran_pca::SimplePcaOptions::irlba_options

Further options to pass to irlba::compute().

◆ num_threads

int scran_pca::SimplePcaOptions::num_threads = 1

Number of threads to use. The parallelization scheme is determined by tatami::parallelize() and irlba::parallelize().

◆ number

int scran_pca::SimplePcaOptions::number = 25

Number of PCs to compute. This should be no greater than the maximum number of PCs, i.e., the smaller dimension of the input matrix, otherwise an error will be thrown. (This error can be avoided by setting irlba::Options::cap_number = true in SimplePcaOptions::irlba_options, in which case only the maximum number of PCs will be reported in the results.)

◆ realize_matrix

bool scran_pca::SimplePcaOptions::realize_matrix = true

Whether to realize tatami::Matrix objects into an appropriate in-memory format before PCA. This is typically faster but increases memory usage.

◆ scale

bool scran_pca::SimplePcaOptions::scale = false

Should genes be scaled to unit variance? Genes with zero variance are ignored.

◆ transpose

bool scran_pca::SimplePcaOptions::transpose = true

Should the PC matrix be transposed on output? If true, the output matrix is column-major with cells in the columns, which is compatible with downstream libscran steps.

The documentation for this struct was generated from the following file:

scran_pca/simple_pca.hpp

Public Attributes