scran_qc::RnaQcBlockedFilters< Float_ > Class Template Reference

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.

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

• scran_qc/rna_quality_control.hpp