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 determined by tatami::parallelize() and irlba::parallelize().

◆ rank

int gsdecon::Options::rank = 1

Rank of the low-rank approximation. Higher values can capture more biological signal at the risk of including more noise. The default value of 1 assumes that each gene set only describes a single coordinated biological function.

◆ 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. This ensures that each gene contributes equally to the PCA, favoring consistent variation across many genes rather than large variation in a few genes.

◆ 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.

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

gsdecon/Options.hpp

Public Attributes