scran_markers
Marker detection for single-cell data
|
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 |
Options for score_markers_summary()
and friends.
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.
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.
bool scran_markers::ScoreMarkersSummaryOptions::compute_auc = true |
Whether to compute the AUC. This only affects the score_markers_summary()
overload that returns a ScoreMarkersSummaryResults
.
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
.
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
.
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
.
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
.
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
.
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
.
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
.
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
.
int scran_markers::ScoreMarkersSummaryOptions::num_threads = 1 |
Number of threads to use. The parallelization scheme is determined by tatami::parallelize()
.
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.
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
.