scran_qc::RnaQcFilters< Float_ > Class Template Reference

Filter for high-quality cells using RNA-based metrics. More...

#include <rna_quality_control.hpp>

Public Member Functions
Float_	get_sum () const
Float_	get_detected () const
const std::vector< Float_ > &	get_subset_proportion () const
Float_ &	get_sum ()
Float_ &	get_detected ()
std::vector< Float_ > &	get_subset_proportion ()
template<typename Sum_ , typename Detected_ , typename Proportion_ , typename Output_ >
void	filter (const std::size_t num, const ComputeRnaQcMetricsBuffers< Sum_, Detected_, Proportion_ > &metrics, Output_ *const output) const
template<typename Sum_ , typename Detected_ , typename Proportion_ , typename Output_ >
void	filter (const ComputeRnaQcMetricsResults< Sum_, Detected_, Proportion_ > &metrics, Output_ *const output) const
template<typename Output_ = unsigned char, typename Sum_ , typename Detected_ , typename Proportion_ >
std::vector< Output_ >	filter (const ComputeRnaQcMetricsResults< Sum_, Detected_, Proportion_ > &metrics) const

Detailed Description

template<typename Float_ = double>
class scran_qc::RnaQcFilters< Float_ >

Filter for high-quality cells using RNA-based metrics.

Template Parameters

Float_

Floating-point type for filter thresholds.

Member Function Documentation

get_sum() [1/2]

template<typename Float_ = double>

Float_ scran_qc::RnaQcFilters< Float_ >::get_sum ( ) const

inline

Returns

Lower threshold to apply to the sums.

get_detected() [1/2]

template<typename Float_ = double>

Float_ scran_qc::RnaQcFilters< Float_ >::get_detected ( ) const

inline

Returns

Lower threshold to apply to the number of detected genes.

get_subset_proportion() [1/2]

template<typename Float_ = double>

const std::vector< Float_ > & scran_qc::RnaQcFilters< Float_ >::get_subset_proportion ( ) const

inline

Returns

Vector of length equal to the number of feature subsets, containing the upper threshold to apply to each subset proportion.

get_sum() [2/2]

template<typename Float_ = double>

Float_ & scran_qc::RnaQcFilters< Float_ >::get_sum ( )

inline

Returns

Lower threshold to apply to the sums.

get_detected() [2/2]

template<typename Float_ = double>

Float_ & scran_qc::RnaQcFilters< Float_ >::get_detected ( )

inline

Returns

Lower threshold to apply to the number of detected genes.

get_subset_proportion() [2/2]

template<typename Float_ = double>

std::vector< Float_ > & scran_qc::RnaQcFilters< Float_ >::get_subset_proportion ( )

inline

Returns

Vector of length equal to the number of feature subsets, containing the upper threshold to apply to each subset proportion.

filter() [1/3]

template<typename Float_ = double>

template<typename Sum_ , typename Detected_ , typename Proportion_ , typename Output_ >

void scran_qc::RnaQcFilters< Float_ >::filter ( const std::size_t num, const ComputeRnaQcMetricsBuffers< Sum_, Detected_, Proportion_ > & metrics, Output_ *const output ) const

inline

Template Parameters

Sum_	Numeric type to store the summed expression.
Detected_	Integer type to store the number of cells.
Proportion_	Floating-point type to store the proportions.
Output_	Boolean type to store the high quality flags.

Parameters

	num	Number of cells.
	metrics	A collection of arrays containing RNA-based QC metrics, filled by compute_rna_qc_metrics(). The feature subsets should be the same as those used in the metrics supplied to compute_rna_qc_filters().
[out]	output	Pointer to an array of length num. On output, this is truthy for cells considered to be of high quality, and false otherwise.

filter() [2/3]

template<typename Float_ = double>

template<typename Sum_ , typename Detected_ , typename Proportion_ , typename Output_ >

void scran_qc::RnaQcFilters< Float_ >::filter ( const ComputeRnaQcMetricsResults< Sum_, Detected_, Proportion_ > & metrics, Output_ *const output ) const

inline

Template Parameters

Sum_	Numeric type to store the summed expression.
Detected_	Integer type to store the number of cells.
Proportion_	Floating-point type to store the proportions.
Output_	Boolean type to store the high quality flags.

Parameters

	metrics	RNA-based QC metrics returned by compute_rna_qc_metrics(). The feature subsets should be the same as those used in the metrics supplied to compute_rna_qc_filters().
[out]	output	Pointer to an array of length num. On output, this is truthy for cells considered to be of high quality, and false otherwise.

filter() [3/3]

template<typename Float_ = double>

template<typename Output_ = unsigned char, typename Sum_ , typename Detected_ , typename Proportion_ >

std::vector< Output_ > scran_qc::RnaQcFilters< Float_ >::filter ( const ComputeRnaQcMetricsResults< Sum_, Detected_, Proportion_ > & metrics ) const

inline

Template Parameters

Output_	Boolean type to store the high quality flags.
Sum_	Numeric type to store the summed expression.
Detected_	Integer type to store the number of cells.
Proportion_	Floating-point type to store the proportions.

Parameters

metrics

RNA-based QC metrics returned by compute_rna_qc_metrics(). The feature subsets should be the same as those used in the metrics supplied to compute_rna_qc_filters().

Returns

Vector of length num, containing the high-quality calls.

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The documentation for this class was generated from the following file:

• scran_qc/rna_quality_control.hpp