scran_norm::ChoosePseudoCountOptions Struct Reference

Options for choose_pseudo_count(). More...

#include <choose_pseudo_count.hpp>

Public Attributes
double	quantile = 0.05
double	max_bias = 0.1
double	min_value = 1

Detailed Description

Options for choose_pseudo_count().

Member Data Documentation

quantile

double scran_norm::ChoosePseudoCountOptions::quantile = 0.05

Quantile to use for finding the smallest/largest size factors. Setting this to zero will use the observed minimum and maximum, though this is usually too extreme in practice. The default is to take the 5th and 95th percentile, yielding a range that is still representative of most cells.

max_bias

double scran_norm::ChoosePseudoCountOptions::max_bias = 0.1

Acceptable upper bound on the log-transformation bias.

min_value

double scran_norm::ChoosePseudoCountOptions::min_value = 1

Minimum value for the pseudo-count returned by choose_pseudo_count(). Defaults to 1 to stabilize near-zero normalized expression values, otherwise these manifest as avoid large negative values.

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

• scran_norm/choose_pseudo_count.hpp