Options for fit_variance_trend(). More...

#include <fit_variance_trend.hpp>

Public Attributes
double	minimum_mean = 0.1

bool	mean_filter = true

bool	transform = true

double	span = 0.3

bool	use_minimum_width = false

double	minimum_width = 1

int	minimum_window_count = 200

int	num_threads = 1

Detailed Description

Options for fit_variance_trend().

Member Data Documentation

◆ minimum_mean

double scran_variances::FitVarianceTrendOptions::minimum_mean = 0.1

Minimum mean log-expression for trend fitting. Genes with lower means are not used in trend fitting, and their fitted values are defined by extrapolating the left edge of the fitted trend is extrapolated to the origin. Only used if FitVarianceTrendOptions::mean_filter = true.

◆ mean_filter

bool scran_variances::FitVarianceTrendOptions::mean_filter = true

Should any filtering be performed on the mean log-expression of each gene (see FitVarianceTrend::minimum_mean)? This may need to be disabled if the trend is not being fitted on statistics computed from log-expression values.

◆ transform

bool scran_variances::FitVarianceTrendOptions::transform = true

Should any transformation of the variances be performed prior to LOWESS smoothing? This may need to be disabled if FitVarianceTrend is not being used on statistics computed from log-expression values.

◆ span

double scran_variances::FitVarianceTrendOptions::span = 0.3

Span for the LOWESS smoother, as a proportion of the total number of points. This is only used if FitVarianceTrendOptions::use_minimum_width = false.

◆ use_minimum_width

bool scran_variances::FitVarianceTrendOptions::use_minimum_width = false

Should a minimum width constraint be applied to the LOWESS smoother? This forces each window to be a minimum width (see FitVarianceTrendOptions::minimum_width) to avoid overfitting from very small windows in high-density intervals. For example, the default smoother performs poorly at high abundances where there are few genes.

◆ minimum_width

double scran_variances::FitVarianceTrendOptions::minimum_width = 1

Minimum width of the window to use when FitVarianceTrendOptions::use_minimum_width = true. This should be appropriate for the range of mean values used in fit_variance_trend(); the default value is chosen based on the typical range in single-cell RNA-seq data.

◆ minimum_window_count

int scran_variances::FitVarianceTrendOptions::minimum_window_count = 200

Minimum number of observations in each window when FitVarianceTrendOptions::use_minimum_width = true. This ensures that each window contains at least a given number of observations for a good fit. If the minimum width window contains fewer observations, it is extended using the standard LOWESS logic until the minimum number is achieved.

◆ num_threads

int scran_variances::FitVarianceTrendOptions::num_threads = 1

Number of threads to use in the LOWESS fit. The parallelization scheme is defined by WeightedLowess::parallelize().

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

scran_variances/fit_variance_trend.hpp

Public Attributes