normalize: Normalize reactivities

In yub18/DESSERT: Differential Analysis of RNA Structure Probing Experiments at Nucleotide Resolution: Uncovering Regulatory Functions of RNA Structure

Normalize reactivities

Description

Remove systematic bias before differential analysis. Skip this step if the user is convinced of the comparability between reactivities.

Usage

normalize(r, fake0 = FALSE, plotfile = FALSE, ncores = "auto", verbose = TRUE)

Arguments

r	Initialized reactivities from init.
fake0	A logical variable indicating whether there are a substantial number of fake 0's in reactivities (FALSE by default). Fake 0's arises when SP experiments fail to measure the structure of part of the nucleotide positions.
plotfile	File name of plot of details. Set to FALSE (default) to skip.
ncores	Number of cores for parallel computation. Automatically determined by default.
verbose	A logical variable indicating whether to print details (TRUE by default).

Details

Users should inspect normalized reactivities carefully.

Value

A list containing the following components:

r	Normalized reactivities.
fit	The fitted model for the normalization.

yub18/DESSERT documentation built on Nov. 5, 2024, 2:36 a.m.