new_EZbakRKinetics

<code>new_EZbakRKinetics</code> efficiently creates an object of class <code>EZbakRKinetics</code>.
It does not perform any rigorous checks of the legitimacy of this object.

A complete rewrite and reimagining of 'bakR' (see 'Vock et al.' (2025) <doi:10.1371/journal.pcbi.1013179>).
Designed to support a wide array of analyses of nucleotide recoding RNA-seq (NR-seq) datasets of any
type, including TimeLapse-seq/SLAM-seq/TUC-seq, Start-TimeLapse-seq (STL-seq),
TT-TimeLapse-seq (TT-TL-seq), and subcellular NR-seq. 'EZbakR' extends
standard NR-seq standard NR-seq mutational modeling to support multi-label analyses
(e.g., 4sU and 6sG dual labeling), and implements an improved hierarchical model to better
account for transcript-to-transcript variance in metabolic label incorporation.
'EZbakR' also generalized dynamical systems modeling of NR-seq data to support analyses
of premature mRNA processing and flow between subcellular compartments. Finally,
'EZbakR' implements flexible and well-powered comparative analyses of all
estimated parameters via design matrix-specified generalized linear modeling.

Isaac Vock

EZbakR

Analyze and Integrate Any Type of Nucleotide Recoding RNA-Seq
Data

new_EZbakRKinetics function

<dl><dt>kinetics</dt>
<dd>Data frame containing information about the kinetic parameters
of interest for each set of features tracked.</dd>
<dt>features</dt>
<dd>Features tracked in <code>kinetics</code> data frame. Needs to be specified
explicitly as it cannot be automatically inferred.</dd>
<dt>metadf</dt>
<dd>Data frame describing each of the samples included</dd>
<dt>name</dt>
<dd>Optional; name to give to fractions table.</dd>
<dt>character_limit</dt>
<dd>Maximum number of characters for naming out fractions output. EZbakR
will try to name this as a "_" separated character vector of all of the features analyzed.
If this name is greater than <code>character_limit</code>, then it will default to "fraction#", where
"#" represents a simple numerical ID for the table.
in <code>kinetics</code></dd></dl>

Arguments

EZbakRKinetics object constructor — new_EZbakRKinetics

<dl>

<dt>kinetics</dt>
<dd>Data frame containing information about the kinetic parameters
of interest for each set of features tracked.</dd>


<dt>features</dt>
<dd>Features tracked in <code>kinetics</code> data frame. Needs to be specified
explicitly as it cannot be automatically inferred.</dd>


<dt>metadf</dt>
<dd>Data frame describing each of the samples included</dd>


<dt>name</dt>
<dd>Optional; name to give to fractions table.</dd>


<dt>character_limit</dt>
<dd>Maximum number of characters for naming out fractions output. EZbakR
will try to name this as a "_" separated character vector of all of the features analyzed.
If this name is greater than <code>character_limit</code>, then it will default to "fraction#", where
"#" represents a simple numerical ID for the table.
in <code>kinetics</code></dd>

</dl>

new_EZbakRKinetics: `EZbakRKinetics` object constructor

Description

Usage

Arguments