EZQC.EZbakRFractions

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

EZQC.EZbakRFractions function

<dl><dt>obj</dt>
<dd>EZbakRFractions object, which is an EZbakRData object on which
<code>EstimateFractions</code> has been run.</dd>
<dt>features</dt>
<dd>Set of features analyzed in the fractions table you are
interested QCing. This gets passed to <code>EZget()</code> to help find this table.</dd>
<dt>populations</dt>
<dd>Set of mutation types analyzed in the fractions table
you are interested in QCing. This gets passed to <code>EZget()</code> to help find this table.</dd>
<dt>fraction_design</dt>
<dd>The fraction "design matrix" specified to get the
fractions table you are interested in QCing. This gets passed to <code>EZget()</code> to
help find this table.</dd>
<dt>...</dt>
<dd>Additional arguments. Currently goes unused.</dd></dl>

Arguments

Run quality control checks — EZQC.EZbakRFractions

<dl>

<dt>obj</dt>
<dd>EZbakRFractions object, which is an EZbakRData object on which
<code>EstimateFractions</code> has been run.</dd>


<dt>features</dt>
<dd>Set of features analyzed in the fractions table you are
interested QCing. This gets passed to <code>EZget()</code> to help find this table.</dd>


<dt>populations</dt>
<dd>Set of mutation types analyzed in the fractions table
you are interested in QCing. This gets passed to <code>EZget()</code> to help find this table.</dd>


<dt>fraction_design</dt>
<dd>The fraction "design matrix" specified to get the
fractions table you are interested in QCing. This gets passed to <code>EZget()</code> to
help find this table.</dd>


<dt>...</dt>
<dd>Additional arguments. Currently goes unused.</dd>

</dl>

EZQC.EZbakRFractions: Run quality control checks

Description

Usage

Value

Arguments