Options for blocked_pca(). More...

#include <blocked_pca.hpp>

Public Attributes
int	number = 25

bool	scale = false

bool	transpose = true

scran_blocks::WeightPolicy	block_weight_policy = scran_blocks::WeightPolicy::VARIABLE

scran_blocks::VariableWeightParameters	variable_block_weight_parameters

bool	components_from_residuals = true

bool	realize_matrix = true

int	num_threads = 1

irlba::Options	irlba_options

Detailed Description

Options for blocked_pca().

Member Data Documentation

◆ block_weight_policy

scran_blocks::WeightPolicy scran_pca::BlockedPcaOptions::block_weight_policy = scran_blocks::WeightPolicy::VARIABLE

Policy to use for weighting batches of different size.

◆ components_from_residuals

bool scran_pca::BlockedPcaOptions::components_from_residuals = true

Compute the principal components from the residuals. If false, only the rotation vector is computed from the residuals, and the original expression values are projected onto the new axes.

◆ irlba_options

irlba::Options scran_pca::BlockedPcaOptions::irlba_options

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

◆ num_threads

int scran_pca::BlockedPcaOptions::num_threads = 1

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

◆ number

int scran_pca::BlockedPcaOptions::number = 25

Number of principal components (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::BlockedPcaOptions::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::BlockedPcaOptions::scale = false

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

◆ transpose

bool scran_pca::BlockedPcaOptions::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.

◆ variable_block_weight_parameters

scran_blocks::VariableWeightParameters scran_pca::BlockedPcaOptions::variable_block_weight_parameters

Parameters for the variable block weights. Only used when BlockedPcaOptions::block_weight_policy = scran_blocks::WeightPolicy::VARIABLE.

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

scran_pca/blocked_pca.hpp

Public Attributes