run_limma_gsea

This internal function implements limma's camera and fry methods for gene set
enrichment analysis with support for covariates.

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_limma_gsea function

<dl><dt>abundance_mat</dt>
<dd>A matrix of abundance data with features as rows and samples as columns</dd>
<dt>metadata</dt>
<dd>A data frame containing sample metadata</dd>
<dt>group</dt>
<dd>A character string specifying the grouping variable column name</dd>
<dt>covariates</dt>
<dd>A character vector of covariate column names (optional)</dd>
<dt>contrast</dt>
<dd>Contrast specification for multi-group comparisons (optional)</dd>
<dt>gene_sets</dt>
<dd>A named list of gene sets (pathway -&gt; gene IDs)</dd>
<dt>method</dt>
<dd>Either "camera" or "fry"</dd>
<dt>inter.gene.cor</dt>
<dd>Inter-gene correlation for camera (default 0.01)</dd>
<dt>min_size</dt>
<dd>Minimum gene set size</dd>
<dt>max_size</dt>
<dd>Maximum gene set size</dd>
<dt>p.adjust.method</dt>
<dd>P-value adjustment method</dd></dl>

Arguments

Run limma-based gene set analysis (camera/fry) — run_limma_gsea

<dl>

<dt>abundance_mat</dt>
<dd>A matrix of abundance data with features as rows and samples as columns</dd>


<dt>metadata</dt>
<dd>A data frame containing sample metadata</dd>


<dt>group</dt>
<dd>A character string specifying the grouping variable column name</dd>


<dt>covariates</dt>
<dd>A character vector of covariate column names (optional)</dd>


<dt>contrast</dt>
<dd>Contrast specification for multi-group comparisons (optional)</dd>


<dt>gene_sets</dt>
<dd>A named list of gene sets (pathway -&gt; gene IDs)</dd>


<dt>method</dt>
<dd>Either "camera" or "fry"</dd>


<dt>inter.gene.cor</dt>
<dd>Inter-gene correlation for camera (default 0.01)</dd>


<dt>min_size</dt>
<dd>Minimum gene set size</dd>


<dt>max_size</dt>
<dd>Maximum gene set size</dd>


<dt>p.adjust.method</dt>
<dd>P-value adjustment method</dd>

</dl>

run_limma_gsea: Run limma-based gene set analysis (camera/fry)

Description

Usage

Value

Arguments