scran_qc::CrisprQcFilters< Float_ > Class Template Reference

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

#include <crispr_quality_control.hpp>

Public Member Functions
Float_	get_max_value () const
Float_ &	get_max_value ()
template<typename Sum_ , typename Detected_ , typename Value_ , typename Index_ , typename Output_ >
void	filter (size_t num, const ComputeCrisprQcMetricsBuffers< Sum_, Detected_, Value_, Index_ > &metrics, Output_ *output) const
template<typename Sum_ , typename Detected_ , typename Value_ , typename Index_ , typename Output_ >
void	filter (const ComputeCrisprQcMetricsResults< Sum_, Detected_, Value_, Index_ > &metrics, Output_ *output) const
template<typename Output_ = uint8_t, typename Sum_ = double, typename Detected_ = int, typename Value_ = double, typename Index_ = int>
std::vector< Output_ >	filter (const ComputeCrisprQcMetricsResults< Sum_, Detected_, Value_, Index_ > &metrics) const

Detailed Description

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

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

Template Parameters

Float_

Floating-point type for filter thresholds.

Instances of this class are typically created by compute_crispr_qc_filters().

Member Function Documentation

get_max_value() [1/2]

template<typename Float_ = double>

Float_ scran_qc::CrisprQcFilters< Float_ >::get_max_value ( ) const

inline

Returns

Lower threshold to apply to the maximum count.

get_max_value() [2/2]

template<typename Float_ = double>

Float_ & scran_qc::CrisprQcFilters< Float_ >::get_max_value ( )

inline

Returns

Lower threshold to apply to the maximum count.

filter() [1/3]

template<typename Float_ = double>

template<typename Sum_ , typename Detected_ , typename Value_ , typename Index_ , typename Output_ >

void scran_qc::CrisprQcFilters< Float_ >::filter ( size_t num, const ComputeCrisprQcMetricsBuffers< Sum_, Detected_, Value_, Index_ > & metrics, Output_ * output ) const

inline

Template Parameters

Sum_	Numeric type to store the summed expression.
Detected_	Integer type to store the number of cells.
Value_	Type of matrix value.
Index_	Type of the matrix indices.
Output_	Boolean type to store the high quality flags.

Parameters

	num	Number of cells.
	metrics	A collection of arrays containing CRISPR-based QC metrics, filled by compute_crispr_qc_metrics().
[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 Value_ , typename Index_ , typename Output_ >

void scran_qc::CrisprQcFilters< Float_ >::filter ( const ComputeCrisprQcMetricsResults< Sum_, Detected_, Value_, Index_ > & metrics, Output_ * output ) const

inline

Template Parameters

Sum_	Numeric type to store the summed expression.
Detected_	Integer type to store the number of cells.
Value_	Type of matrix value.
Index_	Type of the matrix indices.
Output_	Boolean type to store the high quality flags.

Parameters

	metrics	CRISPR-based QC metrics returned by compute_crispr_qc_metrics().
[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 Value_ = double, typename Index_ = int>

std::vector< Output_ > scran_qc::CrisprQcFilters< Float_ >::filter ( const ComputeCrisprQcMetricsResults< Sum_, Detected_, Value_, Index_ > & 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.
Value_	Type of matrix value.
Index_	Type of the matrix indices.

Parameters

metrics

CRISPR-based QC metrics returned by compute_crispr_qc_metrics().

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/crispr_quality_control.hpp