test_genesets_goat_bootstrap

In typical use-cases, one applies <code>test_genesets()</code> instead with parameter <code>method="goat"</code> ,
which in turn will use <code>test_genesets_goat_precomputed</code> (and not this function).

Perform gene set enrichment analyses using the Gene set Ordinal
Association Test (GOAT) algorithm and visualize your
results. Koopmans, F. (2024) <doi:10.1038/s42003-024-06454-5>.

Frank Koopmans

goat

Gene Set Analysis Using the Gene Set Ordinal Association Test

test_genesets_goat_bootstrap function

<dl><dt>genesets</dt>
<dd>see <code>test_genesets_goat_precomputed</code></dd>
<dt>genelist</dt>
<dd>see <code>test_genesets_goat_precomputed</code></dd>
<dt>score_type</dt>
<dd>see <code>test_genesets_goat_precomputed</code></dd>
<dt>niter</dt>
<dd>integer number of bootstrap iterations; at least 10000, at most 5000000</dd>
<dt>verbose</dt>
<dd>boolean, create debug plots</dd></dl>

Arguments

Naive GOAT variant where we estimate null parameters for each geneset size independently — test_genesets_goat_bootstrap

<dl>

<dt>genesets</dt>
<dd>see <code>test_genesets_goat_precomputed</code></dd>


<dt>genelist</dt>
<dd>see <code>test_genesets_goat_precomputed</code></dd>


<dt>score_type</dt>
<dd>see <code>test_genesets_goat_precomputed</code></dd>


<dt>niter</dt>
<dd>integer number of bootstrap iterations; at least 10000, at most 5000000</dd>


<dt>verbose</dt>
<dd>boolean, create debug plots</dd>

</dl>

test_genesets_goat_bootstrap: Naive GOAT variant where we estimate null parameters for each geneset size independently

Description

Usage

Value

Arguments