Thresholds to define outliers on each metric. More...

#include <SuggestCrisprQcFilters.hpp>

Public Member Functions
template<bool overwrite = true, typename Float , typename Integer , typename Output >
void	filter (size_t n, const PerCellCrisprQcMetrics::Buffers< Float, Integer > &buffers, Output *output) const

template<typename Output = uint8_t>
std::vector< Output >	filter (const PerCellCrisprQcMetrics::Results &metrics) const

template<bool overwrite = true, typename Block , typename Float , typename Integer , typename Output >
void	filter_blocked (size_t n, const Block block, const PerCellCrisprQcMetrics::Buffers< Float, Integer > &buffers, Output output) const

template<typename Output = uint8_t, typename Block >
std::vector< Output >	filter_blocked (const PerCellCrisprQcMetrics::Results &metrics, const Block *block) const

Public Attributes
std::vector< double >	max_count

Detailed Description

Thresholds to define outliers on each metric.

SuggestCrisprQcFilters::run() and related methods will suggest some (hopefully) sensible thresholds based on outlier calls. Users can directly modify the thresholds in instances of this class if the default suggestions are not suitable. These thresholds can then be used to generate calls for low-quality cells via the filter() methods.

Member Function Documentation

◆ filter() [1/2]

template<bool overwrite = true, typename Float , typename Integer , typename Output >

void scran::SuggestCrisprQcFilters::Thresholds::filter	(	size_t	n,
		const PerCellCrisprQcMetrics::Buffers< Float, Integer > &	buffers,
		Output *	output
	)		const

inline

Template Parameters

overwrite	Whether to overwrite existing truthy entries in `output`.
Float	Floating point type for the metrics.
Integer	Integer for the metrics.
Output	Boolean type for the low-quality calls.

Parameters

	n	Number of cells.
[in]	buffers	Pointers to arrays of length `n`, containing the per-cell CRISPR-derived metrics. These should be comparable to the values used to create this `Thresholds` object. Only `max_proportion` and `sums` are used; `detected` is ignored and does not need to be set.
[out]	output	Pointer to an array of length `n`, to store the low-quality calls. Values are set to `true` for low-quality cells. If `overwrite = true`, values are set to `false` for high-quality cells, otherwise the existing entry is preserved.

Use filter_blocked() instead for multi-block datasets.

◆ filter() [2/2]

template<typename Output = uint8_t>

std::vector< Output > scran::SuggestCrisprQcFilters::Thresholds::filter ( const PerCellCrisprQcMetrics::Results & metrics ) const

inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Template Parameters

Output Boolean type for the low-quality calls.

Parameters

metrics Collection of arrays of per-cell CRISPR metrics. These should be comparable to the values used to create this Thresholds object. Only max_proportion and sums are used; detected is ignored and does not need to be set.

Returns: Vector of low-quality calls, of length equal to the number of cells in metrics.

◆ filter_blocked() [1/2]

template<bool overwrite = true, typename Block , typename Float , typename Integer , typename Output >

void scran::SuggestCrisprQcFilters::Thresholds::filter_blocked	(	size_t	n,
		const Block *	block,
		const PerCellCrisprQcMetrics::Buffers< Float, Integer > &	buffers,
		Output *	output
	)		const

inline

Template Parameters

Block	Integer type for the block assignments.
Float	Floating point type for the metrics.
Integer	Integer for the metrics.
Output	Boolean type for the low-quality calls.

Parameters

	n	Number of cells.
[in]	block	Pointer to an array of length `n`, containing the block assignment for each cell. This may be `NULL`, in which case all cells are assumed to belong to the same block.
[in]	buffers	Pointers to arrays of length `n`, containing the per-cell CRISPR-derived metrics. These should be comparable to the values used to create this `Thresholds` object. Only `max_proportion` and `sums` are used; `detected` is ignored and does not need to be set.
[out]	output	Pointer to an array of length `n`, to store the low-quality calls. Values are set to `true` for low-quality cells. If `overwrite = true`, values are set to `false` for high-quality cells, otherwise the existing entry is preserved.

◆ filter_blocked() [2/2]

template<typename Output = uint8_t, typename Block >

std::vector< Output > scran::SuggestCrisprQcFilters::Thresholds::filter_blocked	(	const PerCellCrisprQcMetrics::Results &	metrics,
		const Block *	block
	)		const

inline

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Template Parameters

Block	Integer type for the block assignments.
Output	Boolean type for the low-quality calls.

Parameters

	metrics	Collection of arrays of per-cell CRISPR metrics. These should be comparable to the values used to create this `Thresholds` object. Only `max_proportion` and `sums` are used; `detected` is ignored and does not need to be set.
[in]	block	Pointer to an array of length `n`, containing the block assignment for each cell. This may be `NULL`, in which case all cells are assumed to belong to the same block.

Returns: Vector of low-quality calls, of length equal to the number of cells in metrics.

Member Data Documentation

◆ max_count

std::vector<double> scran::SuggestCrisprQcFilters::Thresholds::max_count

Lower thresholds to define small outliers on the maximum count. Each entry contains the threshold used for the corresponding block. For unblocked analyses, this will be of length 1 as all cells are assumed to belong to the same block.

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

scran/quality_control/SuggestCrisprQcFilters.hpp

Public Member Functions

Public Attributes

Detailed Description

Member Function Documentation

◆ filter() [1/2]

◆ filter() [2/2]

◆ filter_blocked() [1/2]

◆ filter_blocked() [2/2]

Member Data Documentation

◆ max_count