Options for model_gene_variances() and friends. More...

#include <model_gene_variances.hpp>

Collaboration diagram for scran_variances::ModelGeneVariancesOptions:

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Public Attributes
FitVarianceTrendOptions	fit_variance_trend_options

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

scran_blocks::VariableWeightParameters	variable_block_weight_parameters

bool	compute_average = true

int	num_threads = 1

Detailed Description

Options for model_gene_variances() and friends.

Member Data Documentation

◆ fit_variance_trend_options

FitVarianceTrendOptions scran_variances::ModelGeneVariancesOptions::fit_variance_trend_options

Options for fitting the mean-variance trend.

◆ block_weight_policy

scran_blocks::WeightPolicy scran_variances::ModelGeneVariancesOptions::block_weight_policy = scran_blocks::WeightPolicy::VARIABLE

Policy to use for weighting the contribution from each block when computing the average for each statistic. Only relevant to model_gene_variances_blocked() overloads where averaged outputs are requested.

The default of scran_blocks::WeightPolicy::VARIABLE is to define equal weights for blocks once they reach a certain size (see ModelGeneVariancesOptions::variable_block_weight_parameters). For smaller blocks, the weight is linearly proportional to its size to avoid outsized contributions from very small blocks.

Other options include scran_blocks::WeightPolicy::EQUAL, where all blocks are equally weighted regardless of size; and scran_blocks::WeightPolicy::NONE, where the contribution of each block is proportional to its size.

◆ variable_block_weight_parameters

scran_blocks::VariableWeightParameters scran_variances::ModelGeneVariancesOptions::variable_block_weight_parameters

Parameters for the variable block weights, including the threshold at which blocks are considered to be large enough to have equal weight. Only relevant to model_gene_variances_blocked() overloads where averaged outputs are requested and ModelGeneVariancesOptions::block_weight_policy = scran_blocks::WeightPolicy::VARIABLE.

◆ compute_average

bool scran_variances::ModelGeneVariancesOptions::compute_average = true

Whether to compute the average of each statistic across blocks. This only affects the model_gene_variances_blocked() method that returns a ModelGeneVariancesBlockedResults object.

◆ num_threads

int scran_variances::ModelGeneVariancesOptions::num_threads = 1

Number of threads to use for the variance calculations and trend fitting. The parallelization scheme is defined by tatami::parallelize().

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

scran_variances/model_gene_variances.hpp