metabomxtr

Version: 1.12.0

Website

https://www.bioconductor.org/packages/release/bioc/html/metabomxtr.html

Description

This bioconductor packages uses the Bernoulli/lognormal mixture-model (Moulton and Halsey, 1995) to formally account for individual metabolite 'missingness". It simultaneously estimates parameters, modeling the probability of a non-missing response and the mean of observed values. To do this it requires the input of the parameter of interest (i.e. the phenotypic difference) and the number of samples per group. The model can be controlled for confounding factors. After the full model containing the parameter of interest has been run, a reduced model without the parameter of interest is run. The significance of the full and reduced models is then compared using nested likelihood chi-squared tests. A results table can then be generated. This package is designed to be run for individual metabolites with missing values, not across the whole dataset.

Functionality

• Post-Processing

Instrument Data Type

• MS/GC-MS
• MS/LC-MS

Approaches

• Untargeted

Computer Skills

Advanced

Software Type

R Package

Interface

Command line interface

Operating System (OS)

• Unix/Linux
• Mac OS
• Windows

Language

R

Dependencies

methods, Biobase

Input Formats - Open

Matrix, Data frame

Input Formats - Proprietary

N/A

Published

2014

Last Updated

2018

License

GPL-2

Paper

http://www.ncbi.nlm.nih.gov/pubmed/25075114

PMID

25075114