scran::PerCellRnaQcMetrics Class Reference

Compute typical per-cell quality control metrics from an RNA count matrix. More...

#include <PerCellRnaQcMetrics.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
PerCellRnaQcMetrics &	set_num_threads (int n=Defaults::num_threads)
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
template<class Matrix , typename Subset = const uint8_t*>
Results	run (const Matrix *mat, const std::vector< Subset > &subsets) const

Detailed Description

Compute typical per-cell quality control metrics from an RNA count matrix.

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

• The total sum of counts 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. This also quantifies the library preparation efficiency, but with a greater focus on capturing the transcriptional complexity.
• The proportion of counts 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 indicate cell damage due to loss of cytoplasmic transcripts. Spike-in proportions can be interpreted in a similar manner.

This class is just a pre-configured wrapper around PerCellQcMetrics, with some careful division of the subset totals to obtain the subset proportions.

Member Function Documentation

set_num_threads()

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

inline

Parameters

n	Number of threads to use.

Returns

A reference to this PerCellRnaQcMetrics object.

run() [1/2]

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

void scran::PerCellRnaQcMetrics::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 an array of values interpretable as booleans.
Float	Floating point type to store the totals.
Integer	Integer type to store the counts and indices.

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	Buffers object in which to store the output. All pointers should be set to non-NULL values.

run() [2/2]

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

Results scran::PerCellRnaQcMetrics::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 PerCellRnaQcMetrics::Results object containing the QC metrics. Subset proportions are returned depending on the subsets.

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

• scran/quality_control/PerCellRnaQcMetrics.hpp