rna_quality_control.hpp File Reference

Simple per-cell QC metrics from an RNA count matrix. More...

#include <vector>
#include <limits>
#include <algorithm>
#include <type_traits>
#include <cstddef>
#include "tatami/tatami.hpp"
#include "find_median_mad.hpp"
#include "per_cell_qc_metrics.hpp"
#include "choose_filter_thresholds.hpp"
#include "utils.hpp"

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Classes
struct	scran_qc::ComputeRnaQcMetricsOptions
	Options for compute_rna_qc_metrics(). More...
struct	scran_qc::ComputeRnaQcMetricsBuffers< Sum_, Detected_, Proportion_ >
	Buffers for compute_rna_qc_metrics(). More...
struct	scran_qc::ComputeRnaQcMetricsResults< Sum_, Detected_, Proportion_ >
	Results of compute_rna_qc_metrics(). More...
struct	scran_qc::ComputeRnaQcFiltersOptions
	Options for compute_rna_qc_filters(). More...
class	scran_qc::RnaQcFilters< Float_ >
	Filter for high-quality cells using RNA-based metrics. More...
class	scran_qc::RnaQcBlockedFilters< Float_ >
	Filter for high-quality cells using RNA-based metrics with blocking. More...

Namespaces
namespace	scran_qc
	Simple quality control for single-cell data.

Functions
template<typename Value_ , typename Index_ , typename Subset_ , typename Sum_ , typename Detected_ , typename Proportion_ >
void	scran_qc::compute_rna_qc_metrics (const tatami::Matrix< Value_, Index_ > &mat, const std::vector< Subset_ > &subsets, const ComputeRnaQcMetricsBuffers< Sum_, Detected_, Proportion_ > &output, const ComputeRnaQcMetricsOptions &options)
template<typename Sum_ = double, typename Detected_ = int, typename Proportion_ = double, typename Value_ , typename Index_ , typename Subset_ >
ComputeRnaQcMetricsResults< Sum_, Detected_, Proportion_ >	scran_qc::compute_rna_qc_metrics (const tatami::Matrix< Value_, Index_ > &mat, const std::vector< Subset_ > &subsets, const ComputeRnaQcMetricsOptions &options)
template<typename Float_ = double, typename Sum_ , typename Detected_ , typename Proportion_ >
RnaQcFilters< Float_ >	scran_qc::compute_rna_qc_filters (const std::size_t num, const ComputeRnaQcMetricsBuffers< Sum_, Detected_, Proportion_ > &metrics, const ComputeRnaQcFiltersOptions &options)
template<typename Float_ = double, typename Sum_ , typename Detected_ , typename Proportion_ >
RnaQcFilters< Float_ >	scran_qc::compute_rna_qc_filters (const ComputeRnaQcMetricsResults< Sum_, Detected_, Proportion_ > &metrics, const ComputeRnaQcFiltersOptions &options)
template<typename Float_ = double, typename Sum_ , typename Detected_ , typename Proportion_ , typename Block_ >
RnaQcBlockedFilters< Float_ >	scran_qc::compute_rna_qc_filters_blocked (const std::size_t num, const ComputeRnaQcMetricsBuffers< Sum_, Detected_, Proportion_ > &metrics, const Block_ *const block, const ComputeRnaQcFiltersOptions &options)
template<typename Float_ = double, typename Sum_ , typename Detected_ , typename Proportion_ , typename Block_ >
RnaQcBlockedFilters< Float_ >	scran_qc::compute_rna_qc_filters_blocked (const ComputeRnaQcMetricsResults< Sum_, Detected_, Proportion_ > &metrics, const Block_ *const block, const ComputeRnaQcFiltersOptions &options)

Detailed Description

Simple per-cell QC metrics from an RNA count matrix.