Options for center_size_factors(). More...

#include <center_size_factors.hpp>

Collaboration diagram for scran_norm::CenterSizeFactorsOptions:

Public Attributes
bool	ignore_invalid = true

double	center = 1

SizeFactorDiagnostics *	diagnostics = NULL

bool	report_final = false

Detailed Description

Options for center_size_factors().

Member Data Documentation

◆ ignore_invalid

bool scran_norm::CenterSizeFactorsOptions::ignore_invalid = true

Whether to ignore invalid size factors when computing the mean size factor, see ComputeMeanSizeFactorOptions::ignore_invalid for details.

Note that setting this option to true does not actually remove any of the invalid size factors. If these are present, users should call sanitize_size_factors() after centering. The diagnostics value in center_size_factors() and center_size_factors_blocked() can be used to determine whether such a call is necessary. (In general, sanitization should be performed after centering so that the replacement size factors do not interfere with the mean calculations.)

◆ center

double scran_norm::CenterSizeFactorsOptions::center = 1

Mean of the size factors after centering. This should almost always be 1, to ensure that the normalized expression values are on roughly the same scale as the original counts. Nonetheless, expert users can change it to some non-unity value.

◆ diagnostics

SizeFactorDiagnostics* scran_norm::CenterSizeFactorsOptions::diagnostics = NULL

Pointer to diagnostics for invalid size factors, passed to ComputeMeanSizeFactorOptions::diagnostics. Ignored if CenterSizeFactorsOptions::ignore_invalid = false.

◆ report_final

bool scran_norm::CenterSizeFactorsOptions::report_final = false

Whether to report the final mean of the size factors, i.e., after centering. If false, the mean of the input size factors is reported instead.

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