scran::ChooseOutlierFilters::Thresholds Struct Reference

Outlier thresholds for QC filtering. More...

#include <ChooseOutlierFilters.hpp>

Public Member Functions
template<bool overwrite = true, typename Input , typename Output >
void	filter (size_t n, Input *input, Output *output) const
template<typename Output = uint8_t, typename Input >
std::vector< Output >	filter (size_t n, const Input *input) const
template<bool overwrite = true, typename Block , typename Input , typename Output >
void	filter_blocked (size_t n, const Block *block, const Input *input, Output *output) const
template<typename Output = uint8_t, typename Block , typename Input >
std::vector< Output >	filter_blocked (size_t n, const Block *block, const Input *input) const

Public Attributes
std::vector< double >	lower
std::vector< double >	upper

Detailed Description

Outlier thresholds for QC filtering.

Member Function Documentation

filter() [1/2]

template<bool overwrite = true, typename Input , typename Output >

void scran::ChooseOutlierFilters::Thresholds::filter ( size_t  n, Input *  input, Output *  output  ) const

inline

Template Parameters

overwrite	Whether to overwrite existing truthy entries in output.
Input	Numeric type for the values.
Output	Boolean type for the outlier calls.

Parameters

	n	Number of observations.
[in]	input	Pointer to an array of length n, containing the values to be filtered.
[out]	output	Pointer to an array of length n, to store the outlier calls. Values are set to true for outliers. If overwrite = true, values are set to false for non-outliers, otherwise the existing entry is preserved.

Use filter_blocked() instead for multi-block datasets.

filter() [2/2]

template<typename Output = uint8_t, typename Input >

std::vector< Output > scran::ChooseOutlierFilters::Thresholds::filter ( size_t  n, const Input *  input  ) 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 outlier calls.
Input	Numeric type for the values.

Parameters

	n	Number of observations.
[in]	input	Pointer to an array of length n, containing the values to be filtered.

Returns

Vector of outlier calls, of length equal to n.

filter_blocked() [1/2]

template<bool overwrite = true, typename Block , typename Input , typename Output >

void scran::ChooseOutlierFilters::Thresholds::filter_blocked ( size_t  n, const Block *  block, const Input *  input, Output *  output  ) const

inline

Template Parameters

overwrite	Whether to overwrite existing truthy entries in output.
Block	Integer type for the block assignments.
Input	Numeric type for the values.
Output	Boolean type for the outlier 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]	input	Pointer to an array of length n, containing the values to be filtered.
[out]	output	Pointer to an array of length n, to store the outlier calls. Values are set to true for outliers. If overwrite = true, values are set to false for non-outliers, otherwise the existing entry is preserved.

filter_blocked() [2/2]

template<typename Output = uint8_t, typename Block , typename Input >

std::vector< Output > scran::ChooseOutlierFilters::Thresholds::filter_blocked ( size_t  n, const Block *  block, const Input *  input  ) 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 outlier calls.
Block	Integer type for the block assignments.
Input	Numeric type for the values.

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]	input	Pointer to an array of length n, containing the values to be filtered.

Returns

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

Member Data Documentation

lower

std::vector<double> scran::ChooseOutlierFilters::Thresholds::lower

Vector of lower thresholds, one per batch. Cells where the relevant QC metric is below this threshold are considered to be low quality. If empty, no lower threshold is to be used.

upper

std::vector<double> scran::ChooseOutlierFilters::Thresholds::upper

Vector of upper thresholds, one per batch. Cells where the relevant QC metric is above this threshold are considered to be low quality. If empty, no upper threshold is to be used.

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

• scran/quality_control/ChooseOutlierFilters.hpp