TransformSnapshot

Under steady state conditions it is straight-forward to estimate s and d. Otherwise, the total levels at some other time point are needed.

Nucleotide conversion sequencing experiments have been
developed to add a temporal dimension to RNA-seq and single-cell RNA-seq. Such
experiments require specialized tools for primary processing such as GRAND-SLAM,
(see 'Jürges et al' <doi:10.1093/bioinformatics/bty256>) and specialized tools for
downstream analyses. 'grandR' provides a comprehensive toolbox for quality control,
kinetic modeling, differential gene expression analysis and visualization of such data.

Florian Erhard

grandR

Comprehensive Analysis of Nucleotide Conversion Sequencing Data

Teresa Rummel

Lygeri Sakellaridi

Kevin Berg

TransformSnapshot function

<dl><dt>ntr</dt>
<dd>the new to total RNA ratio (measured)</dd>
<dt>total</dt>
<dd>the total level of RNA (measured)</dd>
<dt>t</dt>
<dd>the labeling duration</dd>
<dt>t0</dt>
<dd>time before measurement at which f0 is total level (only necessary under non-steady-state conditions)</dd>
<dt>f0</dt>
<dd>total level at t0 (only necessary under non-steady-state conditions)</dd>
<dt>full.return</dt>
<dd>also return the provided parameters</dd></dl>

Arguments

Estimate parameters for a one-shot experiment. — TransformSnapshot

<dl>

<dt>ntr</dt>
<dd>the new to total RNA ratio (measured)</dd>


<dt>total</dt>
<dd>the total level of RNA (measured)</dd>


<dt>t</dt>
<dd>the labeling duration</dd>


<dt>t0</dt>
<dd>time before measurement at which f0 is total level (only necessary under non-steady-state conditions)</dd>


<dt>f0</dt>
<dd>total level at t0 (only necessary under non-steady-state conditions)</dd>


<dt>full.return</dt>
<dd>also return the provided parameters</dd>

</dl>

TransformSnapshot: Estimate parameters for a one-shot experiment.

Description

Usage

Value

Arguments

Details