score_markers_summary.hpp File Reference

Score potential markers by summaries of effect sizes between pairs of groups of cells. More...

#include "scran_blocks/scran_blocks.hpp"
#include "tatami/tatami.hpp"
#include "sanisizer/sanisizer.hpp"
#include "topicks/topicks.hpp"
#include <array>
#include <map>
#include <vector>
#include <optional>
#include "scan_matrix.hpp"
#include "cohens_d.hpp"
#include "simple_diff.hpp"
#include "block_averages.hpp"
#include "summarize_comparisons.hpp"
#include "average_group_stats.hpp"
#include "create_combinations.hpp"
#include "utils.hpp"

Go to the source code of this file.

Classes
struct	scran_markers::ScoreMarkersSummaryOptions
	Options for score_markers_summary() and friends. More...
struct	scran_markers::ScoreMarkersSummaryBuffers< Stat_, Rank_ >
	Buffers for score_markers_summary() and friends. More...
struct	scran_markers::ScoreMarkersSummaryResults< Stat_, Rank_ >
	Results for score_markers_summary() and friends. More...

Namespaces
namespace	scran_markers
	Marker detection for single-cell data.
namespace	scran_markers::internal

Typedefs
template<typename Stat_ , typename Index_ >
using	scran_markers::internal::MinrankTopQueues = std::vector<std::vector<topicks::TopQueue<Stat_, Index_> > >

Functions
template<typename Stat_ , typename Index_ , typename Rank_ >
void	scran_markers::internal::preallocate_minrank_queues (const std::size_t ngroups, std::vector< MinrankTopQueues< Stat_, Index_ > > &all_queues, const std::vector< SummaryBuffers< Stat_, Rank_ > > &summaries, const Index_ limit, const bool keep_ties, const int num_threads)
template<typename Stat_ , typename Index_ , typename Rank_ >
void	scran_markers::internal::compute_summary_stats_per_gene (const Index_ gene, const std::size_t ngroups, const Stat_ *const pairwise_buffer_ptr, std::vector< Stat_ > &summary_buffer, MaybeMultipleQuantiles< Stat_ > &summary_qcalcs, MinrankTopQueues< Stat_, Index_ > &minrank_queues, const std::vector< SummaryBuffers< Stat_, Rank_ > > &summaries)
template<typename Stat_ , typename Index_ , typename Rank_ >
void	scran_markers::internal::report_minrank_from_queues (const Index_ ngenes, const std::size_t ngroups, std::vector< MinrankTopQueues< Stat_, Index_ > > &all_queues, const std::vector< SummaryBuffers< Stat_, Rank_ > > &summaries, const int num_threads, const bool keep_ties)
template<typename Index_ , typename Stat_ , typename Rank_ >
void	scran_markers::internal::process_simple_summary_effects (const Index_ ngenes, const std::size_t ngroups, const std::size_t nblocks, const std::size_t ncombos, const std::vector< Stat_ > &combo_means, const std::vector< Stat_ > &combo_vars, const std::vector< Stat_ > &combo_detected, const double threshold, const BlockAverageInfo< Stat_ > &average_info, const std::optional< std::vector< double > > &summary_quantiles, const Index_ minrank_limit, const bool minrank_keep_ties, const ScoreMarkersSummaryBuffers< Stat_, Rank_ > &output, const int num_threads)
template<typename Index_ , typename Stat_ , typename Rank_ >
ScoreMarkersSummaryBuffers< Stat_, Rank_ >	scran_markers::internal::preallocate_summary_results (const Index_ ngenes, const std::size_t ngroups, ScoreMarkersSummaryResults< Stat_, Rank_ > &store, const ScoreMarkersSummaryOptions &options)
template<bool single_block_, typename Value_ , typename Index_ , typename Group_ , typename Block_ , typename Stat_ , typename Rank_ >
void	scran_markers::internal::score_markers_summary (const tatami::Matrix< Value_, Index_ > &matrix, const std::size_t ngroups, const Group_ *const group, const std::size_t nblocks, const Block_ *const block, const std::size_t ncombos, const std::size_t *const combo, const std::vector< Index_ > &combo_sizes, const ScoreMarkersSummaryOptions &options, const ScoreMarkersSummaryBuffers< Stat_, Rank_ > &output)
template<typename Value_ , typename Index_ , typename Group_ , typename Stat_ , typename Rank_ >
void	scran_markers::score_markers_summary (const tatami::Matrix< Value_, Index_ > &matrix, const Group_ *const group, const ScoreMarkersSummaryOptions &options, const ScoreMarkersSummaryBuffers< Stat_, Rank_ > &output)
template<typename Value_ , typename Index_ , typename Group_ , typename Block_ , typename Stat_ , typename Rank_ >
void	scran_markers::score_markers_summary_blocked (const tatami::Matrix< Value_, Index_ > &matrix, const Group_ *const group, const Block_ *const block, const ScoreMarkersSummaryOptions &options, const ScoreMarkersSummaryBuffers< Stat_, Rank_ > &output)
template<typename Stat_ = double, typename Rank_ = int, typename Value_ , typename Index_ , typename Group_ >
ScoreMarkersSummaryResults< Stat_, Rank_ >	scran_markers::score_markers_summary (const tatami::Matrix< Value_, Index_ > &matrix, const Group_ *const group, const ScoreMarkersSummaryOptions &options)
template<typename Stat_ = double, typename Rank_ = int, typename Value_ , typename Index_ , typename Group_ , typename Block_ >
ScoreMarkersSummaryResults< Stat_, Rank_ >	scran_markers::score_markers_summary_blocked (const tatami::Matrix< Value_, Index_ > &matrix, const Group_ *const group, const Block_ *const block, const ScoreMarkersSummaryOptions &options)

Detailed Description

Score potential markers by summaries of effect sizes between pairs of groups of cells.