run_fgsea

Run fgsea using the recommended fgseaMultilevel method

internal

Provides a convenient way to analyze and visualize 'PICRUSt2' output with pre-defined plots and functions. Allows for generating statistical plots about microbiome functional predictions and offers customization options. Features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. Streamlines the 'PICRUSt2' analysis and visualization process. For more details, see Yang et al. (2023) <doi:10.1093/bioinformatics/btad470>.

Chen Yang

ggpicrust2

Make 'PICRUSt2' Output Analysis and Visualization Easier

run_fgsea function

<dl><dt>ranked_list</dt>
<dd>A named vector of ranking statistics</dd>
<dt>gene_sets</dt>
<dd>A list of pathway gene sets</dd>
<dt>min_size</dt>
<dd>An integer specifying the minimum gene set size</dd>
<dt>max_size</dt>
<dd>An integer specifying the maximum gene set size</dd></dl>

Arguments

Run fgsea using the recommended fgseaMultilevel method — run_fgsea

<dl>

<dt>ranked_list</dt>
<dd>A named vector of ranking statistics</dd>


<dt>gene_sets</dt>
<dd>A list of pathway gene sets</dd>


<dt>min_size</dt>
<dd>An integer specifying the minimum gene set size</dd>


<dt>max_size</dt>
<dd>An integer specifying the maximum gene set size</dd>

</dl>

run_fgsea: Run fgsea using the recommended fgseaMultilevel method

Description

Usage

Value

Arguments