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

#include <score_markers_summary.hpp>

Public Attributes
double	threshold = 0

int	num_threads = 1

int	cache_size = 100

bool	compute_cohens_d = true

bool	compute_auc = true

bool	compute_delta_mean = true

bool	compute_delta_detected = true

bool	compute_min = true

bool	compute_mean = true

bool	compute_median = true

bool	compute_max = true

bool	compute_min_rank = true

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

scran_blocks::VariableWeightParameters	variable_block_weight_parameters

Detailed Description

Options for score_markers_summary() and friends.

Member Data Documentation

◆ block_weight_policy

scran_blocks::WeightPolicy scran_markers::ScoreMarkersSummaryOptions::block_weight_policy = scran_blocks::WeightPolicy::VARIABLE

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

◆ cache_size

int scran_markers::ScoreMarkersSummaryOptions::cache_size = 100

Size of the cache, in terms of the number of pairwise comparisons. Larger values speed up the comparisons at the cost of higher memory consumption.

◆ compute_auc

bool scran_markers::ScoreMarkersSummaryOptions::compute_auc = true

Whether to compute the AUC. This only affects the score_markers_summary() overload that returns a ScoreMarkersSummaryResults.

◆ compute_cohens_d

bool scran_markers::ScoreMarkersSummaryOptions::compute_cohens_d = true

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

◆ compute_delta_detected

bool scran_markers::ScoreMarkersSummaryOptions::compute_delta_detected = true

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

◆ compute_delta_mean

bool scran_markers::ScoreMarkersSummaryOptions::compute_delta_mean = true

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

◆ compute_max

bool scran_markers::ScoreMarkersSummaryOptions::compute_max = true

Whether to report the maximum of the effect sizes for each group. Only affects the score_markers_summary() overload that returns a ScoreMarkersSummaryResults.

◆ compute_mean

bool scran_markers::ScoreMarkersSummaryOptions::compute_mean = true

Whether to report the mean of the effect sizes for each group. Only affects the score_markers_summary() overload that returns a ScoreMarkersSummaryResults.

◆ compute_median

bool scran_markers::ScoreMarkersSummaryOptions::compute_median = true

Whether to report the median of the effect sizes for each group. Only affects the score_markers_summary() overload that returns a ScoreMarkersSummaryResults.

◆ compute_min

bool scran_markers::ScoreMarkersSummaryOptions::compute_min = true

Whether to report the minimum of the effect sizes for each group. Only affects the score_markers_summary() overload that returns a ScoreMarkersSummaryResults.

◆ compute_min_rank

bool scran_markers::ScoreMarkersSummaryOptions::compute_min_rank = true

Whether to report the minimum rank of the effect sizes for each group. Only affects the score_markers_summary() overload that returns a ScoreMarkersSummaryResults.

◆ num_threads

int scran_markers::ScoreMarkersSummaryOptions::num_threads = 1

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

◆ threshold

double scran_markers::ScoreMarkersSummaryOptions::threshold = 0

Threshold on the differences in expression values, used to adjust the Cohen's d and AUC calculations. This should be non-negative.

◆ variable_block_weight_parameters

scran_blocks::VariableWeightParameters scran_markers::ScoreMarkersSummaryOptions::variable_block_weight_parameters

Parameters for the variable block weights. Only used when ScoreMarkersSummaryOptions::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_summary.hpp

Public Attributes