Compute per-cell quality control metrics from a CRISPR guide count matrix. More...

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
PerCellCrisprQcMetrics &	set_num_threads (int n=Defaults::num_threads)

template<class Matrix , typename Float , typename Integer >
void	run (const Matrix *mat, Buffers< Float, Integer > &output) const

template<class Matrix >
Results	run (const Matrix *mat) const

Detailed Description

Compute per-cell quality control metrics from a CRISPR guide count matrix.

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

The total sum of counts for each cell. Low counts indicate that the cell was not successfully transfected with a construct, or that library preparation and sequencing failed. In either case, the cell is considered to be of low quality.
The number of detected guides per cell. In theory, this should be 1, as each cell should express no more than one guide construct. However, ambient contamination may introduce non-zero counts for multiple guides, without necessarily interfering with downstream analyses. As such, this metric is less useful for guide data, though we compute it anyway.
The proportion of counts in the most abundant guide construct. Low values indicate that the cell was transfected with multiple guides. The identity of the most abundant guide is also reported.

Under the hood, this class is just a pre-configured wrapper around PerCellQcMetrics. with some careful division of the maximum count.

Member Function Documentation

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

inline

Parameters

n	Number of threads to use.

template<class Matrix , typename Float , typename Integer >

void scran::PerCellCrisprQcMetrics::run	(	const Matrix *	mat,
		Buffers< Float, Integer > &	output
	)		const

inline

Compute the QC metrics from an CRISPR count matrix.

Template Parameters

Matrix	Type of matrix, usually a `tatami::NumericMatrix`.
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 CRISPR guide counts.
[out]	output	`Buffers` object in which to store the output. All pointers should be set to non-`NULL` values.

template<class Matrix >

Results scran::PerCellCrisprQcMetrics::run ( const Matrix * mat ) const

inline

Compute the QC metrics from an CRISPR count matrix and return the results.

Template Parameters

Matrix Type of matrix, usually a tatami::NumericMatrix.

Parameters

mat	Pointer to a feature-by-cells matrix containing CRISPR counts.

Returns: A PerCellCrisprQcMetrics::Results object containing the QC metrics.

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