Options for choose_highly_variable_genes(). More...

#include <choose_highly_variable_genes.hpp>

Public Attributes
size_t	top = 4000

bool	larger = true

std::pair< bool, double >	bound = std::make_pair<bool, double>(false, 0)

bool	keep_ties = true

Detailed Description

Options for choose_highly_variable_genes().

Member Data Documentation

◆ top

size_t scran_variances::ChooseHighlyVariableGenesOptions::top = 4000

Number of top genes to choose. The actual number of genes may be smaller, if top is greater than the number of genes in the dataset with statistics greater than threshold; or larger, if ChooseHighlyVariableGenesOptions::keep_ties = true.

◆ larger

bool scran_variances::ChooseHighlyVariableGenesOptions::larger = true

Whether larger statistics correspond to higher variances.

◆ bound

std::pair<bool, double> scran_variances::ChooseHighlyVariableGenesOptions::bound = std::make_pair<bool, double>(false, 0)

The first value specifies whether to consider an absolute bound on the statistic when choosing HVGs. The second value is a lower bound for the statistic, at or below which a gene will not be considered as highly variable even if it is among the top top genes. If ChooseHighlyVariableGenesOptions::larger = false, this is an upper bound instead.

◆ keep_ties

bool scran_variances::ChooseHighlyVariableGenesOptions::keep_ties = true

Whether to keep all genes with statistics that are tied with the top-th gene. If false, ties are arbitrarily broken but the number of retained genes will not be greater than top.

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