results

Drop-in replacement for DESeq2's results function for simple settings involving
a single variable. Appends the PsiLFC estimate.

Ratios of count data such as obtained from RNA-seq are modelled
using Bayesian statistics to derive posteriors for effects sizes. This
approach is described in Erhard & Zimmer (2015) <doi:10.1093/nar/gkv696>
and Erhard (2018) <doi:10.1093/bioinformatics/bty471>.

Florian Erhard

Log Fold Change Distribution Tools for Working with Ratios of
Counts

results function

<dl><dt>object</dt>
<dd>the DESeq2DataSet object</dd>
<dt>contrast</dt>
<dd>Vector of length 3, specifying the variable and the two levels
to compute effect sizes for (&lt;name&gt;,&lt;A&gt;,&lt;B&gt;)</dd>
<dt>cre</dt>
<dd>Compute credible intervals as well? (can also be a vector of quantiles)</dd>
<dt>...</dt>
<dd>Handed over to DESeq2's results function</dd></dl>

Arguments

Psi LFC effect size estimator for DESeq2 — results

<dl>

<dt>object</dt>
<dd>the DESeq2DataSet object</dd>


<dt>contrast</dt>
<dd>Vector of length 3, specifying the variable and the two levels
to compute effect sizes for (&lt;name&gt;,&lt;A&gt;,&lt;B&gt;)</dd>


<dt>cre</dt>
<dd>Compute credible intervals as well? (can also be a vector of quantiles)</dd>


<dt>...</dt>
<dd>Handed over to DESeq2's results function</dd>

</dl>

results: Psi LFC effect size estimator for DESeq2

Description

Usage

Value

Arguments