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, 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