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metabolic-module-significance-calculation - Calculate metabolic module significance for sample traits

Calculates module significance statistics to assess if metabolic correlation modules associate with categorical sample traits.

Tags

Updated: 2026-09-19
metabolomicswgcnametabodiffmodule-significancer-packagebioinformatics

Capabilities

Calculate module significance statisticsGenerate module-trait association plotsExtract significant metabolic correlation modulesCompute module eigenmetabolite values

Typical Inputs

MultiAssayExperiment object with normalized metabolite measurementsMetabolite rowData with WGCNA module assignmentsSample colData with categorical trait annotations

Typical Outputs

Module significance statistics per module and traitP-values and effect estimates for module-trait associationsMS_plot visualization of module-trait associations

What this skill does

  • Calculate module significance statistics
  • Generate module-trait association plots
  • Extract significant metabolic correlation modules
  • Compute module eigenmetabolite values

Inputs

  • MultiAssayExperiment object with normalized metabolite measurements
  • Metabolite rowData with WGCNA module assignments
  • Sample colData with categorical trait annotations

Outputs

  • Module significance statistics per module and trait
  • P-values and effect estimates for module-trait associations
  • MS_plot visualization of module-trait associations
  • Metabolite significance values per module
  • Module eigenmetabolite values

Requirements

  • R version 4.0.2 or higher
  • MetaboDiff R package
  • WGCNA R package
  • MultiAssayExperiment R package

Source

  • Spec: SKILL.md

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