mseapca

Version: 1

Website

https://cran.r-project.org/web/packages/mseapca/index.html

Description

Metabolite set enrichment analysis for factor loading in principal component analysis (mseapca), is a CRAN package that provides functions for MSEA and PCA. It is designed so that PCA is used to select metabolites for MSEA, where biological inferences can be made about them. There are three major features in this package. The first creates a list of metabolic pathways (either .csv or KEGG .tar.gz, depending on whether the list is user created or downloaded from KEGG). Secondly, PCA can be performed. This function includes automatic zero, mean and unit variance scaling. Finally MSEA can be performed with overrepresentation analysis (ORA) or using Subramanian et al's method.

Functionality

• Statistical Analysis
• Pathway Analysis/Metabolite Set Enrichment Analysis

Instrument Data Type

• NMR/1D NMR
• NMR/2D 1H NMR
• NMR/13C-HSQC NMR

Approaches

Computer Skills

Advanced

Software Type

• R Package

Interface

• Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

XML

Input Formats - Open

Peaklist (data.frame), Pathway list (.csv, .tar.gz)

Input Formats - Proprietary

N/A

Published

2012

Last Updated

2015

License

BSD

Paper

http://www.ncbi.nlm.nih.gov/pubmed/24555693

PMID

24555693