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 in practice, this is usually too sensitive to outliers. The default is to take the 5th and 95th percentile to obtain a range that captures most of the distribution.

max_bias

double scran_norm::ChoosePseudoCountOptions::max_bias = 0.1

Acceptable upper bound on the log2-transformation bias. This is the magnitude of any spurious log2-fold change between the cells with the smallest and largest size factors.

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.

---

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

• scran_norm/choose_pseudo_count.hpp