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Timothée Flutre edited this page Oct 28, 2013 · 48 revisions

Overview

eQtlBma is a package implementing Bayesian statistical methods aiming at detecting eQTLs jointly in multiple subgroups (e.g. tissues). See the article by Flutre et al (PLoS Genetics, 2013) for the multiple-tissue eQTL study. See the article by Wen & Stephens (Annals of Applied Statistics, 2013) for details on the computations of the Bayes Factor as well as applications on GWAS meta-analysis and multi-population eQTL study (mesh software). See the article by Wen (Biometrics, to appear) for the model handling LD, that is multiple-SNP, multiple-tissue model (sbams software).

Installation

You can retrieve the code by:

Then, it should be possible to easily install the package with the following commands: tar xzvf eqtlbma-1.0.tar.gz; cd eqtlbma-1.0; ./configure; make; make check; make install

If you have any trouble while doing this, it's likely not due to the package itself. Indeed, it uses the GNU Build System (Autotools) in order to be portable. Therefore, any error may rather be due to the fact that your system has versions of the Autotools that are a bit too old. For instance, installing eQtlBma works with Autoconf v >= 2.69, Automake v >= 1.13.1, Libtool v >= 2.4.2 and Texinfo v >= 1.174. To solve this, upgrade your system.

If the installation error persists, maybe you didn't provide enough options required for a successful compilation and linking of the code, e.g. when the GSL >= v1.15 and/or ZLIB >= v1.2.6 are not found. To solve this, read the INSTALL file, or the tips below:

  • If you don't have administrator rights on the machine, you can install the package in your own home: ./configure --prefix=$HOME.
  • If you installed a new version of ZLIB in a custom location (e.g. in /usr/local/lib), you can specify it during the installation: ./configure LDFLAGS=-L/usr/local/lib.
  • If you want to run the tests successfully with make check, you will need R >= 2.15.

In terms of portability, the compilation and installation of the package should work well on any Linux system (say, a computer cluster under Red Hat, a laptop under Ubuntu). Starting with version 1.2.1, the package should also work on Mac OS X (except make check) but beforehand you need to install xcode as well as all the other required packages (gsl, zlib, autotools). Note that the package has not been tested on Windows and we don't plan to do so.

Usage

Thanks to the GNU Build System, it's easy to access the manual of the package in different ways:

  • directly in a terminal via info eqtlbma (the "info" file is created when running make, and is installed when running make install);
  • by opening doc/manual_eqtlbma.pdf with any pdf viewer (after running make pdf);
  • by opening doc/manual_eqtlbma.html/index.html with any internet browser (after running make html).

Note that the manual doesn't describe the methods in details. Instead, read the articles cited above.

Troubleshooting

For anything related to the package, be sure first to read the manual as well as its FAQ. If this doesn't answer your question(s), you can add an issue on Github or contact us directly.

NEWS

See the NEWS file for more details.

  • v1.3 is underway
  • 28/03/2013: v1.2 (v1.2.1 made on 28/10/2013 is the same as v1.2 with small changes for Mac OS X)
  • 08/02/2013: v1.1
  • 16/01/2013: v1.0 (first public release)

Authors

Please let us know if you want to substantially contribute to the code and fork the repository.

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