scran::PerCellQcMetrics Class Reference

Compute a variety of per-cell quality control metrics from a count matrix. More...

#include <PerCellQcMetrics.hpp>

Classes
struct	Buffers
	Buffers for direct storage of the calculated statistics. More...
struct	Defaults
	Default parameters. More...
struct	Results
	Result store for QC metric calculations. More...

Public Member Functions
PerCellQcMetrics &	set_compute_total (bool s=Defaults::compute_total)
PerCellQcMetrics &	set_compute_detected (bool s=Defaults::compute_detected)
PerCellQcMetrics &	set_compute_max_count (bool s=Defaults::compute_max_count)
PerCellQcMetrics &	set_compute_max_index (bool s=Defaults::compute_max_index)
PerCellQcMetrics &	set_compute_subset_total (bool s=Defaults::compute_subset_total)
PerCellQcMetrics &	set_compute_subset_detected (bool s=Defaults::compute_subset_detected)
PerCellQcMetrics &	set_num_threads (int n=Defaults::num_threads)
template<class Matrix , typename Subset = const uint8_t*>
Results	run (const Matrix *mat, const std::vector< Subset > &subsets) const
template<class Matrix , typename Subset = const uint8_t*, typename Float , typename Integer >
void	run (const Matrix *mat, const std::vector< Subset > &subsets, Buffers< Float, Integer > &output) const

Detailed Description

Compute a variety of per-cell quality control metrics from a count matrix.

Given a feature-by-cell count matrix, this class computes several QC metrics:

• The total sum for each cell, which represents the efficiency of library preparation and sequencing. Low totals indicate that the library was not successfully captured.
• The number of detected features (i.e., with non-zero counts). This also quantifies the library preparation efficiency, but with a greater focus on capturing the transcriptional complexity.
• The maximum count across all features. This is useful in situations where only one feature is expected to be present, e.g., CRISPR guides, hash tags.
• The row index of the feature with the maximum count. If multiple features are tied for the maximum count, the earliest feature is reported.
• The total count in pre-defined feature subsets. The exact interpretation depends on the nature of the subset - most commonly, one subset will contain all genes on the mitochondrial chromosome, where higher proportions of counts in the mitochondrial subset indicate cell damage due to loss of cytoplasmic transcripts. Spike-in proportions can be interpreted in a similar manner.
• The number of detected features in pre-defined feature subsets. Analogous to the number of detected features for the entire feature space.

These calculations are done in a single pass, avoiding the need to reload data from the count matrix.

Member Function Documentation

set_compute_total()

PerCellQcMetrics & scran::PerCellQcMetrics::set_compute_total ( bool  s = Defaults::compute_total )

inline

Parameters

s	Whether to compute the total count for each cell. This option only affects the run() method that returns a Results object.

Returns

Reference to this PerCellQcMetrics object.

set_compute_detected()

PerCellQcMetrics & scran::PerCellQcMetrics::set_compute_detected ( bool  s = Defaults::compute_detected )

inline

Parameters

s	Whether to compute the number of detected features for each cell. This option only affects the run() method that returns a Results object.

Returns

Reference to this PerCellQcMetrics object.

set_compute_max_count()

PerCellQcMetrics & scran::PerCellQcMetrics::set_compute_max_count ( bool  s = Defaults::compute_max_count )

inline

Parameters

s	Whether to compute the maximmum count for each cell. This option only affects the run() method that returns a Results object.

Returns

Reference to this PerCellQcMetrics object.

set_compute_max_index()

PerCellQcMetrics & scran::PerCellQcMetrics::set_compute_max_index ( bool  s = Defaults::compute_max_index )

inline

Parameters

s	Whether to store the index of the feature with the maximum count for each cell. This option only affects the run() method that returns a Results object.

Returns

Reference to this PerCellQcMetrics object.

set_compute_subset_total()

PerCellQcMetrics & scran::PerCellQcMetrics::set_compute_subset_total ( bool  s = Defaults::compute_subset_total )

inline

Parameters

s	Whether to compute the total count in each feature subset. This option only affects the run() method that returns a Results object.

Returns

Reference to this PerCellQcMetrics object.

set_compute_subset_detected()

PerCellQcMetrics & scran::PerCellQcMetrics::set_compute_subset_detected ( bool  s = Defaults::compute_subset_detected )

inline

Parameters

s	Whether to compute the number of detected features in each feature subset. This option only affects the run() method that returns a Results object.

Returns

Reference to this PerCellQcMetrics object.

set_num_threads()

PerCellQcMetrics & scran::PerCellQcMetrics::set_num_threads ( int  n = Defaults::num_threads )

inline

Parameters

n	Number of threads to use.

Returns

Reference to this PerCellQcMetrics object.

run() [1/2]

template<class Matrix , typename Subset = const uint8_t*>

Results scran::PerCellQcMetrics::run ( const Matrix *  mat, const std::vector< Subset > &  subsets  ) const

inline

Compute the QC metrics from an input matrix and return the results.

Template Parameters

Matrix	Type of matrix, usually a tatami::NumericMatrix.
Subset	Pointer to an array of values interpretable as booleans.

Parameters

	mat	Pointer to a feature-by-cells tatami matrix containing counts.
[in]	subsets	Vector of pointers to arrays of length equal to mat->nrow(). Each array represents a feature subset and indicating whether each feature in mat belongs to that subset. Users can pass {} if no subsets are to be used.

Returns

A Results object containing the QC metrics. Subset totals are returned depending on the subsets.

run() [2/2]

template<class Matrix , typename Subset = const uint8_t*, typename Float , typename Integer >

void scran::PerCellQcMetrics::run ( const Matrix *  mat, const std::vector< Subset > &  subsets, Buffers< Float, Integer > &  output  ) const

inline

Compute the QC metrics from an input matrix.

Template Parameters

Matrix	Type of matrix, usually a tatami::NumericMatrix.
Subset	Pointer to a type interpretable as boolean.

Parameters

	mat	Pointer to a feature-by-cells matrix containing counts.
[in]	subsets	Vector of pointers to arrays of length equal to mat->nrow(). Each array represents a feature subset and indicating whether each feature in mat belongs to that subset. Users can pass {} if no subsets are to be used.
[out]	output	A Buffers object in which the computed statistics are to be stored.

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

• scran/quality_control/PerCellQcMetrics.hpp