control_normalize: Control Settings for Counts Normalization

In insightsengineering/hermes: Preprocessing, analyzing, and reporting of RNA-seq data

Control Settings for Counts Normalization

Description

This control function allows for easy customization of the normalization settings.

Usage

control_normalize(
  log = TRUE,
  lib_sizes = NULL,
  prior_count = 1,
  fit_type = "parametric"
)

Arguments

log	(flag) whether log2 values are returned, otherwise original scale is used.
lib_sizes	(NULL or counts) library sizes, if NULL the vector with the sum of the counts for each of the samples will be used.
prior_count	(non-negative number) average count to be added to each observation to avoid taking log of zero, used only when log = TRUE.
fit_type	(string) method to estimate dispersion parameters in Negative Binomial model, used only when normalize() methods include vst and/or rlog. See estimateDispersions for details.

Value

List with the above settings used to perform the normalization procedure.

Note

To be used with the normalize() function.

Examples

control_normalize()
control_normalize(log = FALSE, lib_sizes = rep(1e6L, 20))

insightsengineering/hermes documentation built on Sept. 19, 2024, 9:06 p.m.