Software review

MADAM - An open source meta-analysis toolbox for R and Bioconductor

Karl G Kugler , Laurin AJ Mueller and Armin Graber

Institute for Bioinformatics and Translational Research, UMIT, Eduard Wallnöfer-Zentrum 1, Hall in Tirol, 6060, Austria

author email corresponding author email

Source Code for Biology and Medicine 2010, 5:3doi:10.1186/1751-0473-5-3

Published:	1 March 2010

Abstract

Background

Meta-analysis is a major theme in biomedical research. In the present paper we introduce a package for R and Bioconductor that provides useful tools for performing this type of work. One idea behind the development of MADAM was that many meta-analysis methods, which are available in R, are not able to use the capacities of parallel computing yet. In this first version, we implemented one meta-analysis method in such a parallel manner. Additionally, we provide tools for combining the results from a set of methods in an ensemble approach. Functionality for visualization of results is also provided.

Results

The presented package enables the carrying out of meta-analysis either by providing functions directly or by wrapping them to existing implementations. Overall, five different meta-analysis methods are now usable through MADAM, along with another three methods for combining the corresponding results. Visualizing the results is eased by three included functions. For developing and testing meta-analysis methods, a mock up data generator is integrated.

Conclusions

The use of MADAM enables a user to focus on one package, in turn enabling them to work with the same data types across a set of methods. By making use of the snow package, MADAM can be made compatible with an existing parallel computing infrastructure. MADAM is open source and freely available within CRAN http://cran.r-project.org webcite.