demo_multiomics_analysis {SUMO}R Documentation

Demonstration of SUMO Utility in Multi-Omics Analysis using MOFA2

Description

Run a complete MOFA2-based analysis pipeline using either SUMO-generated or real-world CLL multi-omics data. This function includes preprocessing, MOFA model training, variance decomposition visualization, and optional PowerPoint report generation.

Usage

demo_multiomics_analysis(
  data_type = c("SUMO", "real_world"),
  export_pptx = TRUE,
  verbose = TRUE
)

Arguments

data_type

Character. Options are "SUMO" for synthetic data or "real_world" for the CLL dataset.

export_pptx

Logical. If TRUE, saves a PowerPoint summary of the analysis. Default is TRUE.

verbose

Logical. If TRUE, prints progress messages. Default is TRUE.

Details

PowerPoint generation is skipped if required packages (officer, rvg, and ⁠systemfonts >= 1.1.0⁠) are not available.

Value

Invisibly returns the trained MOFA model object.

See Also

simulate_twoOmicsData(), plot_factor(), plot_weights()

Examples

if (
  requireNamespace("MOFA2", quietly = TRUE) &&
  requireNamespace("MOFAdata", quietly = TRUE) &&
  requireNamespace("systemfonts", quietly = TRUE) &&
  utils::packageVersion("systemfonts") >= "1.1.0" &&
  identical(Sys.getenv("NOT_CRAN"), "true")
) {
  demo_multiomics_analysis("SUMO", export_pptx = FALSE)
  demo_multiomics_analysis("real_world", export_pptx = FALSE)
}


[Package SUMO version 1.2.0 Index]