Helper for delayed log-normalization. More...

#include <normalize_counts.hpp>

Inheritance diagram for scran_norm::DelayedLogNormalizeHelper< OutputValue_, InputValue_, Index_, SizeFactors_ >:

Collaboration diagram for scran_norm::DelayedLogNormalizeHelper< OutputValue_, InputValue_, Index_, SizeFactors_ >:

Public Member Functions
	DelayedLogNormalizeHelper (SizeFactors_ size_factors, OutputValue_ log_base, OutputValue_ pseudo_count)

std::optional< Index_ >	nrow () const

std::optional< Index_ >	ncol () const

bool	zero_depends_on_row () const

bool	zero_depends_on_column () const

bool	non_zero_depends_on_row () const

bool	non_zero_depends_on_column () const

void	dense (const bool row, const Index_ idx, const Index_ start, const Index_ length, const InputValue_ input, OutputValue_ const output) const

void	dense (const bool row, const Index_ idx, const std::vector< Index_ > &indices, const InputValue_ input, OutputValue_ const output) const

bool	is_sparse () const

void	sparse (const bool row, const Index_ idx, const Index_ number, const InputValue_ input_value, const Index_ const index, OutputValue_ *const output_value) const

OutputValue_	fill (const bool row, const Index_ idx) const

Public Member Functions inherited from tatami::DelayedUnaryIsometricOperationHelper< OutputValue_, InputValue_, Index_ >

Detailed Description

template<typename OutputValue_, typename InputValue_, typename Index_, typename SizeFactors_>
class scran_norm::DelayedLogNormalizeHelper< OutputValue_, InputValue_, Index_, SizeFactors_ >

Helper for delayed log-normalization.

This is a helper subclass that performs scaling normalization and log-transformation for each cell in tatami::DelayedUnaryIsometricOperation. It should be constructed with normalize_counts() and is equivalent to chaining tatami::DelayedUnaryIsometricDivideVectorHelper (for the scaling by size factors), with tatami::DelayedUnaryIsometricLog1pHelper and tatami::DelayedUnaryIsometricDivideScalarHelper (for log-transformation with a pseudo-count of 1 and an arbitrary base) or tatami::DelayedUnaryIsometricAddScalarHelper and tatami::DelayedUnaryIsometricCustomLogHelper (for log-transformation with a non-unity pseudo-count).

Template Parameters

OutputValue_	Type of the result of the operation.
InputValue_	Type of the matrix value used in the operation.
Index_	Integer type for the row/column indices.
SizeFactors_	Container for the size factors. This should support `[]`, `size()`, `begin()` and `end()`.

Constructor & Destructor Documentation

◆ DelayedLogNormalizeHelper()

template<typename OutputValue_ , typename InputValue_ , typename Index_ , typename SizeFactors_ >

scran_norm::DelayedLogNormalizeHelper< OutputValue_, InputValue_, Index_, SizeFactors_ >::DelayedLogNormalizeHelper	(	SizeFactors_	size_factors,
		OutputValue_	log_base,
		OutputValue_	pseudo_count )

inline

Parameters

vector	Vector of size factors, of length equal to the number of columns.
log_base	Base of the log, usually 2.
pseudo_count	Pseudo-count to add before log-transformation, usually 1.

Member Function Documentation

◆ nrow()

template<typename OutputValue_ , typename InputValue_ , typename Index_ , typename SizeFactors_ >

std::optional< Index_ > scran_norm::DelayedLogNormalizeHelper< OutputValue_, InputValue_, Index_, SizeFactors_ >::nrow ( ) const

inlinevirtual

Implements tatami::DelayedUnaryIsometricOperationHelper< OutputValue_, InputValue_, Index_ >.

◆ ncol()

template<typename OutputValue_ , typename InputValue_ , typename Index_ , typename SizeFactors_ >

std::optional< Index_ > scran_norm::DelayedLogNormalizeHelper< OutputValue_, InputValue_, Index_, SizeFactors_ >::ncol ( ) const

inlinevirtual

Implements tatami::DelayedUnaryIsometricOperationHelper< OutputValue_, InputValue_, Index_ >.

◆ zero_depends_on_row()

template<typename OutputValue_ , typename InputValue_ , typename Index_ , typename SizeFactors_ >

bool scran_norm::DelayedLogNormalizeHelper< OutputValue_, InputValue_, Index_, SizeFactors_ >::zero_depends_on_row ( ) const

inlinevirtual

Implements tatami::DelayedUnaryIsometricOperationHelper< OutputValue_, InputValue_, Index_ >.

◆ zero_depends_on_column()

template<typename OutputValue_ , typename InputValue_ , typename Index_ , typename SizeFactors_ >

bool scran_norm::DelayedLogNormalizeHelper< OutputValue_, InputValue_, Index_, SizeFactors_ >::zero_depends_on_column ( ) const

inlinevirtual

Implements tatami::DelayedUnaryIsometricOperationHelper< OutputValue_, InputValue_, Index_ >.

◆ non_zero_depends_on_row()

template<typename OutputValue_ , typename InputValue_ , typename Index_ , typename SizeFactors_ >

bool scran_norm::DelayedLogNormalizeHelper< OutputValue_, InputValue_, Index_, SizeFactors_ >::non_zero_depends_on_row ( ) const

inlinevirtual

Implements tatami::DelayedUnaryIsometricOperationHelper< OutputValue_, InputValue_, Index_ >.

◆ non_zero_depends_on_column()

template<typename OutputValue_ , typename InputValue_ , typename Index_ , typename SizeFactors_ >

bool scran_norm::DelayedLogNormalizeHelper< OutputValue_, InputValue_, Index_, SizeFactors_ >::non_zero_depends_on_column ( ) const

inlinevirtual

Implements tatami::DelayedUnaryIsometricOperationHelper< OutputValue_, InputValue_, Index_ >.

◆ dense() [1/2]

template<typename OutputValue_ , typename InputValue_ , typename Index_ , typename SizeFactors_ >

void scran_norm::DelayedLogNormalizeHelper< OutputValue_, InputValue_, Index_, SizeFactors_ >::dense	(	const bool	row,
		const Index_	idx,
		const Index_	start,
		const Index_	length,
		const InputValue_ *	input,
		OutputValue_ *const	output ) const

inlinevirtual

Implements tatami::DelayedUnaryIsometricOperationHelper< OutputValue_, InputValue_, Index_ >.

◆ dense() [2/2]

template<typename OutputValue_ , typename InputValue_ , typename Index_ , typename SizeFactors_ >

void scran_norm::DelayedLogNormalizeHelper< OutputValue_, InputValue_, Index_, SizeFactors_ >::dense	(	const bool	row,
		const Index_	idx,
		const std::vector< Index_ > &	indices,
		const InputValue_ *	input,
		OutputValue_ *const	output ) const

inlinevirtual

Implements tatami::DelayedUnaryIsometricOperationHelper< OutputValue_, InputValue_, Index_ >.

◆ is_sparse()

template<typename OutputValue_ , typename InputValue_ , typename Index_ , typename SizeFactors_ >

bool scran_norm::DelayedLogNormalizeHelper< OutputValue_, InputValue_, Index_, SizeFactors_ >::is_sparse ( ) const

inlinevirtual

Implements tatami::DelayedUnaryIsometricOperationHelper< OutputValue_, InputValue_, Index_ >.

◆ sparse()

template<typename OutputValue_ , typename InputValue_ , typename Index_ , typename SizeFactors_ >

void scran_norm::DelayedLogNormalizeHelper< OutputValue_, InputValue_, Index_, SizeFactors_ >::sparse	(	const bool	row,
		const Index_	idx,
		const Index_	number,
		const InputValue_ *	input_value,
		const Index_ *const	index,
		OutputValue_ *const	output_value ) const

inlinevirtual

Implements tatami::DelayedUnaryIsometricOperationHelper< OutputValue_, InputValue_, Index_ >.

◆ fill()

template<typename OutputValue_ , typename InputValue_ , typename Index_ , typename SizeFactors_ >

OutputValue_ scran_norm::DelayedLogNormalizeHelper< OutputValue_, InputValue_, Index_, SizeFactors_ >::fill	(	const bool	row,
		const Index_	idx ) const

inlinevirtual

Implements tatami::DelayedUnaryIsometricOperationHelper< OutputValue_, InputValue_, Index_ >.

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

scran_norm/normalize_counts.hpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ DelayedLogNormalizeHelper()

Member Function Documentation

◆ nrow()

◆ ncol()

◆ zero_depends_on_row()

◆ zero_depends_on_column()

◆ non_zero_depends_on_row()

◆ non_zero_depends_on_column()

◆ dense() [1/2]

◆ dense() [2/2]

◆ is_sparse()

◆ sparse()

◆ fill()