get_normalized_read_counts

get_normalized_read_counts.EZbakRFractions

get_normalized_read_counts.EZbakRData

Uses TMM normalization strategy, similar to that used by DESeq2 and edgeR.

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

get_normalized_read_counts function

<dl><dt>obj</dt>
<dd>An <code>EZbakRData</code> or <code>EZbakRFractions</code> object.</dd>
<dt>features_to_analyze</dt>
<dd>Features in relevant table</dd>
<dt>fractions_name</dt>
<dd>Name of fractions table to use</dd>
<dt>feature_lengths</dt>
<dd>Table of effective lengths for each feature combination in your
data. For example, if your analysis includes features named GF and XF, this
should be a data frame with columns GF, XF, and length.</dd>
<dt>scale_factors</dt>
<dd>Dataframe with two columns, one being "sample" (sample names)
and the other being "scale_factor" (value to divide read counts by to normalize them)</dd></dl>

Arguments

<ul>
<li><code>get_normalized_read_counts(EZbakRFractions)</code>: Method for class EZbakRFractions
Get normalized read counts from fractions table.</li>
<li><code>get_normalized_read_counts(EZbakRData)</code>: Method for class EZbakRData
Get normalized read counts from a cB table.</li>
</ul>

Methods (by class)

Get normalized read counts from either a cB table or EZbakRFractions object. — get_normalized_read_counts

<dl>

<dt>obj</dt>
<dd>An <code>EZbakRData</code> or <code>EZbakRFractions</code> object.</dd>


<dt>features_to_analyze</dt>
<dd>Features in relevant table</dd>


<dt>fractions_name</dt>
<dd>Name of fractions table to use</dd>


<dt>feature_lengths</dt>
<dd>Table of effective lengths for each feature combination in your
data. For example, if your analysis includes features named GF and XF, this
should be a data frame with columns GF, XF, and length.</dd>


<dt>scale_factors</dt>
<dd>Dataframe with two columns, one being "sample" (sample names)
and the other being "scale_factor" (value to divide read counts by to normalize them)</dd>

</dl>

get_normalized_read_counts: Get normalized read counts from either a cB table or `EZbakRFractions` object.

Description

Usage

Value

Arguments

Methods (by class)

Examples