scran::ChooseHvgs Class Reference

Choose highly variable genes for downstream analyses. More...

#include <ChooseHvgs.hpp>

Classes
struct	Defaults
	Default paramater settings. More...

Public Member Functions
ChooseHvgs &	set_top (size_t t=Defaults::top)
template<typename V , typename T >
void	run (size_t n, const V *statistic, T *output) const
template<typename T = uint8_t, typename V >
std::vector< T >	run (size_t n, const V *statistic) const

Detailed Description

Choose highly variable genes for downstream analyses.

This is done by selecting the top number of genes with the largest values for a precomputed variance statistic. We typically use the residual from the trend as computed by ModelGeneVar.

Member Function Documentation

set_top()

ChooseHvgs & scran::ChooseHvgs::set_top ( size_t  t = Defaults::top )

inline

Parameters

t	The number of top genes to consider as highly variable genes.

Returns

A reference to this ChooseHvgs object.

The choice is more or less arbitrary and is a trade-off between capturing more biological signal at the cost of increasing noise. Values of 1000-5000 seem appropriate for most use cases. Note that increasing the number of genes will also increase the size of the subdataset to be used in downstream computation.

run() [1/2]

template<typename V , typename T >

void scran::ChooseHvgs::run ( size_t  n, const V *  statistic, T *  output  ) const

inline

Choose HVGs to use in downstream analyses.

Template Parameters

V	Type of the variance statistic.
T	Type to be used as a boolean.

Parameters

	n	Number of genes.
[in]	statistic	Pointer to an array of length n containing the per-gene variance statistics.
[out]	output	Pointer to an array of length n, used to store a boolean flag. On completion, output is filled with true if the gene is to be retained and false otherwise.

run() [2/2]

template<typename T = uint8_t, typename V >

std::vector< T > scran::ChooseHvgs::run ( size_t  n, const V *  statistic  ) const

inline

Template Parameters

V	Type of the variance statistic.
T	Type to be used as a boolean.

Parameters

	n	Number of genes.
[in]	statistic	Pointer to an array of length n containing the per-gene variance statistics.

Returns

A vector of booleans of length n, indicating whether each gene is to be retained.

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

• scran/feature_selection/ChooseHvgs.hpp