Options for choose_highly_variable_genes(). More...

#include <choose_highly_variable_genes.hpp>

Public Attributes
std::size_t	top = 4000

bool	larger = true

bool	use_bound = true

double	bound = 0

bool	keep_ties = true

Detailed Description

Options for choose_highly_variable_genes().

Member Data Documentation

◆ top

std::size_t scran_variances::ChooseHighlyVariableGenesOptions::top = 4000

Number of top genes to choose. Note that the actual number of chosen genes may be:

smaller than top, if the latter is greater than the total number of genes in the dataset.
smaller than top, if ChooseHighlyVariableGenesOptions::use_bound = true and top is greater than N, where N is the number of genes in the dataset with statistics greater than ChooseHighlyVariableGenesOptions::bound (or less than the bound, if ChosenHighlyVariableGenesOptions::larger = false).
larger than top, if ChooseHighlyVariableGenesOptions::keep_ties = true and there are multiple ties with the top-th chosen gene.

◆ larger

bool scran_variances::ChooseHighlyVariableGenesOptions::larger = true

Whether larger statistics correspond to higher variability, i.e., the genes with the top top largest statistics should be chosen.

◆ use_bound

bool scran_variances::ChooseHighlyVariableGenesOptions::use_bound = true

Whether to consider an absolute bound on the statistic when choosing HVGs. The value of the bound is determined by ChooseHighlyVariableGenesOptions::bound.

◆ bound

double scran_variances::ChooseHighlyVariableGenesOptions::bound = 0

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. Only used if ChooseHighlyVariableGenesOptions::use_bound = true. If ChooseHighlyVariableGenesOptions::larger = false, this is an upper bound instead.

The default of zero assumes that the input statistics are residuals from a mean-variance trend (see fit_variance_trend()), in which case all chosen HVGs should have positive residuals.

◆ keep_ties

bool scran_variances::ChooseHighlyVariableGenesOptions::keep_ties = true

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

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

scran_variances/choose_highly_variable_genes.hpp