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

#include <rna_quality_control.hpp>

Public Member Functions
const std::vector< Float_ > &	get_sum () const

const std::vector< Float_ > &	get_detected () const

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

std::vector< Float_ > &	get_sum ()

std::vector< Float_ > &	get_detected ()

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

template<typename Index_ , typename Sum_ , typename Detected_ , typename Proportion_ , typename Block_ , typename Output_ >
void	filter (Index_ num, const ComputeRnaQcMetricsBuffers< Sum_, Detected_, Proportion_ > &metrics, const Block_ block, Output_ output) const

template<typename Sum_ , typename Detected_ , typename Proportion_ , typename Block_ , typename Output_ >
void	filter (const ComputeRnaQcMetricsResults< Sum_, Detected_, Proportion_ > &metrics, const Block_ block, Output_ output) const

template<typename Output_ = uint8_t, typename Sum_ = double, typename Detected_ = int, typename Proportion_ = double, typename Block_ = int>
std::vector< Output_ >	filter (const ComputeRnaQcMetricsResults< Sum_, Detected_, Proportion_ > &metrics, const Block_ *block) const

Detailed Description

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

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

Template Parameters

Float_ Floating-point type for filter thresholds.

Member Function Documentation

◆ get_sum() [1/2]

template<typename Float_ = double>

const std::vector< Float_ > & scran_qc::RnaQcBlockedFilters< Float_ >::get_sum ( ) const

inline

Returns: Vector of length equal to the number of blocks, containing the lower threshold on the sums in each block.

◆ get_detected() [1/2]

template<typename Float_ = double>

const std::vector< Float_ > & scran_qc::RnaQcBlockedFilters< Float_ >::get_detected ( ) const

inline

Returns: Vector of length equal to the number of blocks, containing the lower threshold on the number of detected genes in each block.

◆ get_subset_proportion() [1/2]

template<typename Float_ = double>

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

inline

Returns: Vector of length equal to the number of blocks. Each entry is a vector of length equal to the number of feature subsets, containing the upper threshold to apply to the each subset proportion.

◆ get_sum() [2/2]

template<typename Float_ = double>

std::vector< Float_ > & scran_qc::RnaQcBlockedFilters< Float_ >::get_sum ( )

inline

Returns: Vector of length equal to the number of blocks, containing the lower threshold on the sums in each block.

◆ get_detected() [2/2]

template<typename Float_ = double>

std::vector< Float_ > & scran_qc::RnaQcBlockedFilters< Float_ >::get_detected ( )

inline

Returns: Vector of length equal to the number of blocks, containing the lower threshold on the number of detected genes in each block.

◆ get_subset_proportion() [2/2]

template<typename Float_ = double>

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

inline

Returns: Vector of length equal to the number of feature subsets. Each entry is a vector of length equal to the number of blocks, containing the upper threshold to apply to the subset proportion for that block.

◆ filter() [1/3]

template<typename Float_ = double>

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

void scran_qc::RnaQcBlockedFilters< Float_ >::filter	(	Index_	num,
		const ComputeRnaQcMetricsBuffers< Sum_, Detected_, Proportion_ > &	metrics,
		const Block_ *	block,
		Output_ *	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.
Block_	Integer type for the block assignment.
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()`.
[in]	block	Pointer to an array of length `num` containing block identifiers. Each identifier should correspond to the same blocks used in the constructor.
[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 Block_ , typename Output_ >

void scran_qc::RnaQcBlockedFilters< Float_ >::filter	(	const ComputeRnaQcMetricsResults< Sum_, Detected_, Proportion_ > &	metrics,
		const Block_ *	block,
		Output_ *	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.
Block_	Integer type for the block assignment.
Output_	Boolean type to store the high quality flags.

Parameters

	metrics	RNA-based QC metrics computed by `compute_rna_qc_metrics()`. The feature subsets should be the same as those used in the `metrics` supplied to `compute_rna_qc_filters()`.
[in]	block	Pointer to an array of length `num` containing block identifiers. Each identifier should correspond to the same blocks used in the constructor.
[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_ = uint8_t, typename Sum_ = double, typename Detected_ = int, typename Proportion_ = double, typename Block_ = int>

std::vector< Output_ > scran_qc::RnaQcBlockedFilters< Float_ >::filter	(	const ComputeRnaQcMetricsResults< Sum_, Detected_, Proportion_ > &	metrics,
		const Block_ *	block ) 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.
Block_	Integer type for the block assignment.

Parameters

	metrics	RNA-based QC metrics computed by `compute_rna_qc_metrics()`. The feature subsets should be the same as those used in the `metrics` supplied to `compute_rna_qc_filters()`.
[in]	block	Pointer to an array of length `num` containing block identifiers. Each identifier should correspond to the same blocks used in the constructor.

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

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

scran_qc/rna_quality_control.hpp

Public Member Functions

Detailed Description

Member Function Documentation

◆ get_sum() [1/2]

◆ get_detected() [1/2]

◆ get_subset_proportion() [1/2]

◆ get_sum() [2/2]

◆ get_detected() [2/2]

◆ get_subset_proportion() [2/2]

◆ filter() [1/3]

◆ filter() [2/3]

◆ filter() [3/3]