mseapca (version 2.2.1)

ora_all: ORA using all metabolites

Description

This function performs over-representation analysis (ORA) using all metabolites present in the given metabolite set list as the background, without specifying a reference metabolome. This corresponds to the behavior of MetaboAnalyst when no reference metabolome is uploaded.

Usage

ora_all(SIG, M)

Value

A list with:

Result of MSEA(ORA)

Matrix of p-values and q-values

significant metabolites

List of significant metabolites per set

Contingency tables

A list of 2×2 contingency tables used in Fisher's exact tests.

Arguments

SIG

Character vector of significant metabolites

M

Named list of metabolite sets

Author

Hiroyuki Yamamoto

References

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

Yamamoto H. Probabilistic Over-Representation Analysis for Metabolite Set Enrichment Analysis Considering Undetected Metabolites", Jxiv, (2024).

Examples

# Example: Metabolome data
data(fasting_mseapca)

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

# Perform ORA using detected metabolites only
B <- ora_all(SIG, M)
B$`Result of MSEA(ORA)`