Options for sanitize_size_factors(). More...

#include <sanitize_size_factors.hpp>

Public Attributes
SanitizeAction	handle_zero = SanitizeAction::ERROR

SanitizeAction	handle_negative = SanitizeAction::ERROR

SanitizeAction	handle_nan = SanitizeAction::ERROR

SanitizeAction	handle_infinite = SanitizeAction::ERROR

Detailed Description

Options for sanitize_size_factors().

Member Data Documentation

◆ handle_zero

SanitizeAction scran_norm::SanitizeSizeFactorsOptions::handle_zero = SanitizeAction::ERROR

How should we handle size factors of zero?

If set to SANITIZE, they will be automatically set to the smallest valid size factor (or 1, if all size factors are invalid). This ensures that the normalized values will be large to reflect the extremity of the scaling, but still finite for sensible downstream processing.

In most cases, size factors of zero are only obtained for cells with all-zero counts. By replacing the size factor with a finite value, we ensure that any all-zero cells are represented by all-zero columns in the normalized matrix, which is a reasonable outcome if those cells cannot be filtered out during upstream quality control.

◆ handle_negative

SanitizeAction scran_norm::SanitizeSizeFactorsOptions::handle_negative = SanitizeAction::ERROR

How should we handle negative size factors?

If set to SANITIZE, they will be automatically set to the smallest valid size factor (or 1, if all size factors are invalid), following the same logic as SanitizeSizeFactorsOptions::handle_zero.

◆ handle_nan

SanitizeAction scran_norm::SanitizeSizeFactorsOptions::handle_nan = SanitizeAction::ERROR

How should we handle NaN size factors?

If set to `SANITIZE, NaN size factors will be automatically set to 1, meaning that scaling is a no-op.

◆ handle_infinite

SanitizeAction scran_norm::SanitizeSizeFactorsOptions::handle_infinite = SanitizeAction::ERROR

How should we handle infinite size factors?

If set to SANITIZE, infinite size factors will be automatically set to the largest valid size factor (or 1, if all size factors are invalid). This ensures that any normalized values will be, at least, finite; the choice of a relatively large replacement value reflects the extremity of the scaling.

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