mseapca2.2.1 package

Metabolite Set Enrichment Analysis for Loadings

csv2list

Convert metabolite set / csv to list

list2xml

Save compound set as XML file

msea_ora_range

Wrapper function for Over-Representation Analysis with p-value range e...

msea_ora

Wrapper function for over-representation analysis (ORA)

msea_sub

MSEA by Subramanian et al.

ora_all

ORA using all metabolites

ora_bino

Over-representation analysis with binomial resampling adjustment

ora_det

ORA using detected metabolites

ora_est

ORA adjusting for undetected metabolites

ora_full

Over-representation analysis with full enumeration of undetected metab...

pathbank2list

Generate metabolite set list from PathBank database

read_pathway

Read metabolite set file (*.xml)

setlabel

Generate binary label matrix of metabolite set

ssea_ora

Single sample enrichment analysis by over representation analysis

Download source packageRead PDF manual

Computing metabolite set enrichment analysis (MSEA) (Yamamoto, H. et al. (2014) <doi:10.1186/1471-2105-15-51>), single sample enrichment analysis (SSEA) (Yamamoto, H. (2023) <doi:10.51094/jxiv.262>) and over-representation analysis (ORA) that accounts for undetected metabolites (Yamamoto, H. (2024) <doi:10.51094/jxiv.954>).

  • Maintainer: Hiroyuki Yamamoto
  • License: LGPL-3
  • Last published: 2025-07-05