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

#include <score_markers_summary.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	compute_min = true

bool	compute_mean = true

bool	compute_median = true

bool	compute_max = true

bool	compute_min_rank = true

std::size_t	min_rank_limit = 500

bool	min_rank_preserve_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_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.

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.

◆ 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_group_detected

bool scran_markers::ScoreMarkersSummaryOptions::compute_group_detected = true

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

◆ compute_group_mean

bool scran_markers::ScoreMarkersSummaryOptions::compute_group_mean = true

Whether to compute the mean expression in each group. 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.

◆ min_rank_limit

std::size_t scran_markers::ScoreMarkersSummaryOptions::min_rank_limit = 500

Limit on the reported minimum rank. If a gene has a minimum rank greater than min_rank_limit, its reported minimum rank will be set to the number of genes. Lower values improve memory efficiency but discard all ranking information beyond min_rank_limit.

◆ min_rank_preserve_ties

bool scran_markers::ScoreMarkersSummaryOptions::min_rank_preserve_ties = false

Whether to preserve ties when computing the minimum rank. If true, tied genes with equal effect sizes receive the same rank within each pairwise comparison. Otherwise, ties are broken in a stable manner, i.e., genes in earlier rows will receive a higher rank.

◆ 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. 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::ScoreMarkersSummaryOptions::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 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