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

#include <score_markers_pairwise.hpp>

Public Attributes
double	threshold = 0

int	num_threads = 1

bool	compute_group_mean = true

bool	compute_group_detected = true

bool	compute_cohens_d = true

bool	compute_auc = true

bool	compute_delta_mean = true

bool	compute_delta_detected = true

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

Detailed Description

Options for score_markers_pairwise() and friends.

Member Data Documentation

◆ block_average_policy

BlockAveragePolicy scran_markers::ScoreMarkersPairwiseOptions::block_average_policy = BlockAveragePolicy::MEAN

Policy to use for averaging statistics across blocks into a single value. This can either be BlockAveragePolicy::MEAN (weighted mean) or BlockAveragePolicy::QUANTILE (quantile). Only used in score_markers_pairwise_blocked().

◆ block_quantile

double scran_markers::ScoreMarkersPairwiseOptions::block_quantile = 0.5

Quantile probability for summarizing statistics across blocks. Only used in score_markers_pairwise_blocked() when ScoreMarkersPairwiseOptions::block_average_policy = BlockAveragePolicy::QUANTILE.

◆ block_weight_policy

scran_blocks::WeightPolicy scran_markers::ScoreMarkersPairwiseOptions::block_weight_policy = scran_blocks::WeightPolicy::VARIABLE

Policy to use for weighting blocks when computing average statistics/effect sizes across blocks.

The default of scran_blocks::WeightPolicy::VARIABLE is to define equal weights for blocks once they reach a certain size (see ScoreMarkersPairwiseOptions::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.

Only used in score_markers_pairwise_blocked() when ScoreMarkersPairwiseOptions::block_average_policy = BlockAveragePolicy::MEAN.

◆ compute_auc

bool scran_markers::ScoreMarkersPairwiseOptions::compute_auc = true

Whether to compute the AUC. This only affects the score_markers_pairwise() overload that returns a ScoreMarkersPairwiseResults.

◆ compute_cohens_d

bool scran_markers::ScoreMarkersPairwiseOptions::compute_cohens_d = true

Whether to compute Cohen's d. This only affects the score_markers_pairwise() overload that returns a ScoreMarkersPairwiseResults.

◆ compute_delta_detected

bool scran_markers::ScoreMarkersPairwiseOptions::compute_delta_detected = true

Whether to compute the difference in the detected proportion. This only affects the score_markers_pairwise() overload that returns a ScoreMarkersPairwiseResults.

◆ compute_delta_mean

bool scran_markers::ScoreMarkersPairwiseOptions::compute_delta_mean = true

Whether to compute the difference in means. This only affects the score_markers_pairwise() overload that returns a ScoreMarkersPairwiseResults.

◆ compute_group_detected

bool scran_markers::ScoreMarkersPairwiseOptions::compute_group_detected = true

Whether to compute the proportion of cells with detected expression in each group. This only affects the score_markers_pairwise() overload that returns a ScoreMarkersPairwiseResults.

◆ compute_group_mean

bool scran_markers::ScoreMarkersPairwiseOptions::compute_group_mean = true

Whether to compute the mean expression in each group. This only affects the score_markers_pairwise() overload that returns a ScoreMarkersPairwiseResults.

◆ num_threads

int scran_markers::ScoreMarkersPairwiseOptions::num_threads = 1

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

◆ threshold

double scran_markers::ScoreMarkersPairwiseOptions::threshold = 0

Threshold on the differences in expression values between groups, used to adjust the Cohen's d and AUC calculations. This should be non-negative. Higher thresholds will favor genes with large differences at the expense of those with low variance.

◆ variable_block_weight_parameters

scran_blocks::VariableWeightParameters scran_markers::ScoreMarkersPairwiseOptions::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 used in score_markers_pairwise_blocked() when ScoreMarkersPairwiseOptions::block_average_policy = BlockAveragePolicy::MEAN and ScoreMarkersPairwiseOptions::block_weight_policy = scran_blocks::WeightPolicy::VARIABLE.

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

/github/workspace/include/scran_markers/score_markers_pairwise.hpp

Public Attributes