padjust_genesets

Adjust p-values for all genesets, grouped by 'source' then adjust for the number of 'sources'

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

padjust_genesets function

<dl><dt>genesets</dt>
<dd>tibble with genesets, must contain column 'pvalue'</dd>
<dt>method</dt>
<dd>method for multiple testing correction, must be any of <code><a href="/link/stats%3A%3Ap.adjust.methods?package=goat&version=1.1.2" data-mini-rdoc="goat::stats::p.adjust.methods">stats::p.adjust.methods</a></code>, e.g. "BH" or "bonferroni"</dd>
<dt>cutoff</dt>
<dd>numeric cutoff value for adjusted p-value, <code>signif</code> column is set to TRUE for all values lesser-equals</dd>
<dt>correct_sources</dt>
<dd>apply Bonferroni adjustment to all p-values according to the number of geneset sources that were tested. Boolean parameter, set TRUE to enable (default) or FALSE to disable</dd></dl>

Arguments

Adjust p-values for all genesets, grouped by 'source' then adjust for the number of 'sources' — padjust_genesets

<dl>

<dt>genesets</dt>
<dd>tibble with genesets, must contain column 'pvalue'</dd>


<dt>method</dt>
<dd>method for multiple testing correction, must be any of <code><a href='https://rdrr.io/r/stats/p.adjust.html'>stats::p.adjust.methods</a></code>, e.g. "BH" or "bonferroni"</dd>


<dt>cutoff</dt>
<dd>numeric cutoff value for adjusted p-value, <code>signif</code> column is set to TRUE for all values lesser-equals</dd>


<dt>correct_sources</dt>
<dd>apply Bonferroni adjustment to all p-values according to the number of geneset sources that were tested. Boolean parameter, set TRUE to enable (default) or FALSE to disable</dd>

</dl>

padjust_genesets: Adjust p-values for all genesets, grouped by 'source' then adjust for the number of 'sources'

Description

Usage

Value

Arguments