fasting_mseapca: Metabolome data from a fasting mouse study

In mseapca: Metabolite Set Enrichment Analysis for Loadings

Metabolome data from a fasting mouse study

Description

Example data derived from a fasting mouse liver metabolomics study, originally published by Yamamoto et al. and distributed in the loadings package as fasting. This version is reformatted and annotated to reproduce the analysis setup used in MetaboAnalyst. It is intended for demonstrating ORA and MSEA functions in the mseapca package.

Usage

data(fasting_mseapca)

Format

A named list with the following components:

SIG

Character vector of significant metabolites (e.g., p < 0.05).

DET

Character vector of all detected metabolites.

pathway

Named list of metabolite sets (pathways). Each element is a character vector of metabolite IDs belonging to that pathway.

Details

The dataset is intended for vignette examples:

• SIG — Significant metabolites (p < 0.05) obtained from statistical analysis of a fasting vs control comparison.

• DET — Background list of all detected metabolites.

• pathway — Pathway definitions from MetaboAnalyst, reused for mouse data.

The object can be used directly with functions such as msea_ora, ora_det, and ora_bino.

Source

Derived from the fasting dataset in the loadings package.

Original reference: Yamamoto H., Fujimori T., Sato H., Ishikawa G., Kami K., Ohashi Y. (2014). "Statistical hypothesis testing of factor loading in principal component analysis and its application to metabolite set enrichment analysis". BMC Bioinformatics, 15(1):51.

Examples

## Load data
data(fasting_mseapca)

SIG <- fasting_mseapca$SIG
DET <- fasting_mseapca$DET
M   <- fasting_mseapca$pathway

## Simple ORA on detected metabolites
res <- ora_det(SIG, DET, M)
head(res$`Result of MSEA(ORA)`)

mseapca documentation built on Aug. 8, 2025, 7:20 p.m.