scran::quick_grouped_size_factors::Options< Block_, SizeFactor_ > Struct Template Reference

Options for run(). More...

#include <quick_grouped_size_factors.hpp>

Public Attributes
int	rank = 25
std::function< size_t(size_t)>	clusters
const Block_ *	block = NULL
const SizeFactor_ *	initial_factors = NULL
int	num_threads = 1

Detailed Description

template<typename Block_ = int, typename SizeFactor_ = double>
struct scran::quick_grouped_size_factors::Options< Block_, SizeFactor_ >

Options for run().

Template Parameters

Block_	Integer type for the blocking factor.
SizeFactor_	Floating-point type for initial size factors.

Member Data Documentation

rank

template<typename Block_ = int, typename SizeFactor_ = double>

int scran::quick_grouped_size_factors::Options< Block_, SizeFactor_ >::rank = 25

Number of principal components of the log-expression matrix to retain for clustering.

clusters

template<typename Block_ = int, typename SizeFactor_ = double>

std::function<size_t(size_t)> scran::quick_grouped_size_factors::Options< Block_, SizeFactor_ >::clusters

Number of k-means clusters to obtain, as a function of the number of cells in each block. This defaults to the square root with an upper bound of 50.

block

template<typename Block_ = int, typename SizeFactor_ = double>

const Block_* scran::quick_grouped_size_factors::Options< Block_, SizeFactor_ >::block = NULL

Pointer to an array of length equal to the number of cells. Each entry should contain the block assignment for each cell, as an integer in where is the total number of blocks. If NULL, all cells are assumed to belong to a single block.

initial_factors

template<typename Block_ = int, typename SizeFactor_ = double>

const SizeFactor_* scran::quick_grouped_size_factors::Options< Block_, SizeFactor_ >::initial_factors = NULL

Pointer to an array of length equal to the number of cells. Each entry should contain an initial size factor for each cell. If NULL, the initial size factors are defined by LogNormCounts.

num_threads

template<typename Block_ = int, typename SizeFactor_ = double>

int scran::quick_grouped_size_factors::Options< Block_, SizeFactor_ >::num_threads = 1

Number of threads to use in all internal calculations.

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

• scran/normalization/quick_grouped_size_factors.hpp