topicks Namespace Reference

Pick top genes from their statistics. More...

Classes
struct	PickTopGenesOptions
	Options for pick_top_genes(). More...
class	TopQueue
	Priority queue for retaining top genes. More...
struct	TopQueueOptions
	Options for TopQueue. More...

Functions
template<typename Stat_ , typename Bool_ >
void	pick_top_genes (const std::size_t n, const Stat_ *const statistic, const std::size_t top, const bool larger, Bool_ *const output, const PickTopGenesOptions< Stat_ > &options)
template<typename Bool_ , typename Stat_ >
std::vector< Bool_ >	pick_top_genes (const std::size_t n, const Stat_ *const statistic, const std::size_t top, const bool larger, const PickTopGenesOptions< Stat_ > &options)
template<typename Index_ , typename Stat_ >
std::vector< Index_ >	pick_top_genes_index (const Index_ n, const Stat_ *const statistic, const Index_ top, const bool larger, const PickTopGenesOptions< Stat_ > &options)

Detailed Description

Pick top genes from their statistics.

Function Documentation

pick_top_genes() [1/2]

template<typename Stat_ , typename Bool_ >

void topicks::pick_top_genes	(	const std::size_t	n,
		const Stat_ *const	statistic,
		const std::size_t	top,
		const bool	larger,
		Bool_ *const	output,
		const PickTopGenesOptions< Stat_ > &	options )

Template Parameters

Stat_	Numeric type of the statistic for picking top genes.
Bool_	Output boolean type.

Parameters

	n	Number of genes.
[in]	statistic	Pointer to an array of length n, containing the statistics with which to rank genes.
	top	Number of top genes to choose.
	larger	Whether the top genes are defined as those with larger statistics.
[out]	output	Pointer to an array of length n. On output, the i-th element will be true if gene i is one of the top genes and false otherwise. Note that the actual number of chosen genes may be smaller/larger than top, depending on n and options.
	options	Further options.

pick_top_genes() [2/2]

template<typename Bool_ , typename Stat_ >

std::vector< Bool_ > topicks::pick_top_genes	(	const std::size_t	n,
		const Stat_ *const	statistic,
		const std::size_t	top,
		const bool	larger,
		const PickTopGenesOptions< Stat_ > &	options )

Template Parameters

Bool_	Output boolean type.
Stat_	Numeric type of the statistic for picking top genes.

Parameters

	n	Number of genes.
[in]	statistic	Pointer to an array of length n, containing the statistics with which to rank genes.
	top	Number of top genes to choose.
	larger	Whether the top genes are defined as those with larger statistics.
	options	Further options.

Returns

A vector of booleans of length n, indicating whether each gene is to be retained. Note that the actual number of chosen genes may be smaller/larger than top, depending on n and options.

pick_top_genes_index()

template<typename Index_ , typename Stat_ >

std::vector< Index_ > topicks::pick_top_genes_index	(	const Index_	n,
		const Stat_ *const	statistic,
		const Index_	top,
		const bool	larger,
		const PickTopGenesOptions< Stat_ > &	options )

Template Parameters

Index_	Integer type of the output indices.
Stat_	Numeric type of the statistic for picking top genes.

Parameters

	n	Number of genes.
[in]	statistic	Pointer to an array of length n containing the statistics with which to rank genes.
	top	Number of top genes to choose.
	larger	Whether the top genes are defined as those with larger statistics.
	options	Further options.

Returns

Vector of sorted and unique indices for the chosen genes. All indices are guaranteed to be non-negative and less than n. Note that the actual number of chosen genes may be smaller/larger than top, depending on n and options.