gsdecon::Options Struct Reference

Options for compute() and compute_blocked(). More...

#include <Options.hpp>

Public Attributes
int	rank = 1
bool	scale = false
scran_blocks::WeightPolicy	block_weight_policy = scran_blocks::WeightPolicy::VARIABLE
scran_blocks::VariableWeightParameters	variable_block_weight_parameters
int	num_threads = 1
bool	realize_matrix = true
irlba::Options	irlba_options

Detailed Description

Options for compute() and compute_blocked().

Member Data Documentation

block_weight_policy

scran_blocks::WeightPolicy gsdecon::Options::block_weight_policy = scran_blocks::WeightPolicy::VARIABLE

Policy to use for weighting batches of different size, for compute_blocked().

irlba_options

irlba::Options gsdecon::Options::irlba_options

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

num_threads

int gsdecon::Options::num_threads = 1

Number of threads to use. The parallelization scheme is defined by scran_pca::SimplePcaOptions::num_threads (for compute()) or scran_pca::BlockedPcaOptions::num_threads (for compute_blocked()).

rank

int gsdecon::Options::rank = 1

Rank of the low-rank approximation.

realize_matrix

bool gsdecon::Options::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 gsdecon::Options::scale = false

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

variable_block_weight_parameters

scran_blocks::VariableWeightParameters gsdecon::Options::variable_block_weight_parameters

Parameters for the variable block weights for compute_blocked(). Only used when Options::block_weight_policy = scran_blocks::WeightPolicy::VARIABLE.

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

• gsdecon/Options.hpp