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

In ggpicrust2: Make 'PICRUSt2' Output Analysis and Visualization Easier

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

Description

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

Usage

run_limma_gsea(
  abundance_mat,
  metadata,
  group,
  covariates = NULL,
  contrast = NULL,
  gene_sets,
  method = "camera",
  inter.gene.cor = 0.01,
  min_size = 5,
  max_size = 500,
  p.adjust.method = "BH"
)

Arguments

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

Value

A data frame containing gene set analysis results

ggpicrust2 documentation built on April 10, 2026, 5:06 p.m.