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

BlockAveragePolicy	block_average_policy = BlockAveragePolicy::MEAN

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

scran_blocks::VariableWeightParameters	variable_block_weight_parameters

double	block_quantile = 0.5

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_average_policy

BlockAveragePolicy scran_variances::ModelGeneVariancesOptions::block_average_policy = BlockAveragePolicy::MEAN

Policy to use for averaging statistics across blocks. Only relevant to model_gene_variances_blocked(). Ignored for overloads accepting ModelGeneVariancesBlockedBuffers where all entries in average are NULL.

◆ block_weight_policy

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

Policy for weighting the contribution from each block when computing the mean for each statistic. Only relevant to model_gene_variances_blocked() when ModelGeneVariancesOptions::average_policy = BlockAveragePolicy::MEAN.

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() when ModelGeneVariancesOptions::average_policy = BlockAveragePolicy::MEAN. and ModelGeneVariancesOptions::block_weight_policy = scran_blocks::WeightPolicy::VARIABLE.

◆ block_quantile

double scran_variances::ModelGeneVariancesOptions::block_quantile = 0.5

Quantile to use as an "average" statistic across blocks. Only relevant to model_gene_variances_blocked() when ModelGeneVariancesOptions::average_policy = BlockAveragePolicy::QUANTILE. Defaults to 0.5, a.k.a., the median.

◆ 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

Public Attributes