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

#include <score_markers_best.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

bool	largest_cohens_d = true

bool	largest_auc = true

bool	largest_delta_mean = true

bool	largest_delta_detected = true

std::optional< double >	threshold_cohens_d = 0

std::optional< double >	threshold_auc = 0.5

std::optional< double >	threshold_delta_mean = 0

std::optional< double >	threshold_delta_detected = 0

bool	keep_ties = false

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

scran_blocks::VariableWeightParameters	variable_block_weight_parameters

Detailed Description

Options for score_markers_best() and friends.

Member Data Documentation

◆ block_weight_policy

scran_blocks::WeightPolicy scran_markers::ScoreMarkersBestOptions::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 ScoreMarkersBestOptions::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.

◆ compute_auc

bool scran_markers::ScoreMarkersBestOptions::compute_auc = true

Whether to compute the AUC.

◆ compute_cohens_d

bool scran_markers::ScoreMarkersBestOptions::compute_cohens_d = true

Whether to compute Cohen's d.

◆ compute_delta_detected

bool scran_markers::ScoreMarkersBestOptions::compute_delta_detected = true

Whether to compute the delta-detected, i.e., difference in the detected proportion.

◆ compute_delta_mean

bool scran_markers::ScoreMarkersBestOptions::compute_delta_mean = true

Whether to compute the delta-mean, i.e., difference in means.

◆ compute_group_detected

bool scran_markers::ScoreMarkersBestOptions::compute_group_detected = true

Whether to compute the proportion of cells with detected expression in each group.

◆ compute_group_mean

bool scran_markers::ScoreMarkersBestOptions::compute_group_mean = true

Whether to compute the mean expression in each group.

◆ keep_ties

bool scran_markers::ScoreMarkersBestOptions::keep_ties = false

Whether to report genes with effect sizes that are tied with the top-th gene.

◆ largest_auc

bool scran_markers::ScoreMarkersBestOptions::largest_auc = true

Whether to keep the genes with the largest AUC. If false, the genes with the smallest AUC are retained instead.

◆ largest_cohens_d

bool scran_markers::ScoreMarkersBestOptions::largest_cohens_d = true

Whether to keep the genes with the largest Cohen's d. If false, the genes with the smallest Cohen's d are retained instead.

◆ largest_delta_detected

bool scran_markers::ScoreMarkersBestOptions::largest_delta_detected = true

Whether to keep the genes with the largest delta-detected. If false, the genes with the smallest delta-detected are retained instead.

◆ largest_delta_mean

bool scran_markers::ScoreMarkersBestOptions::largest_delta_mean = true

Whether to keep the genes with the largest delta-mean. If false, the genes with the smallest delta-mean are retained instead.

◆ num_threads

int scran_markers::ScoreMarkersBestOptions::num_threads = 1

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

◆ threshold

double scran_markers::ScoreMarkersBestOptions::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.

◆ threshold_auc

std::optional<double> scran_markers::ScoreMarkersBestOptions::threshold_auc = 0.5

The threshold on the AUC. Genes are only retained if their AUC is greater (if ScoreMarkersBestOptions::largest_auc = true) or less than this bound (otherwise). If missing, no threshold is applied on the AUC.

◆ threshold_cohens_d

std::optional<double> scran_markers::ScoreMarkersBestOptions::threshold_cohens_d = 0

The threshold on the Cohen's d. Genes are only retained if their Cohen's d is greater (if ScoreMarkersBestOptions::largest_cohens_d = true) or less than this bound (otherwise). If missing, no threshold is applied on the Cohen's d.

◆ threshold_delta_detected

std::optional<double> scran_markers::ScoreMarkersBestOptions::threshold_delta_detected = 0

The threshold on the delta-detected. Genes are only retained if their delta-detected is greater (if ScoreMarkersBestOptions::largest_delta_detected = true) or less than this bound (otherwise). If missing, no threshold is applied on the delta-detected.

◆ threshold_delta_mean

std::optional<double> scran_markers::ScoreMarkersBestOptions::threshold_delta_mean = 0

The threshold on the delta-mean. Genes are only retained if their delta-mean is greater (if ScoreMarkersBestOptions::largest_delta_mean = true) or less than this bound (otherwise). If missing, no threshold is applied on the delta-mean.

◆ variable_block_weight_parameters

scran_blocks::VariableWeightParameters scran_markers::ScoreMarkersBestOptions::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 when ScoreMarkersBestOptions::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_best.hpp

Public Attributes