Add MeV+R as a BASE extension?

[Jari Häkkinen]

It may be interesting to use MeV+R for visualizing and running R scripts. Could MeV+R be added as an extension to BASE like MeV ... or should MeV+R be an extenssion to the BASE MeV extenstion?

MeV+R web site is ​http://expression.washington.edu/mevr/ and the research paper is open access through ​http://dx.doi.org/10.1186/gb-2008-9-7-r118

MeV+R: using MeV as a graphical user interface for Bioconductor
applications in microarray analysis

Abstract

We present MeV+R, an integration of the JAVA MultiExperiment Viewer
program with Bioconductor packages. This integration of
MultiExperiment Viewer and R is easily extensible to other R
packages and provides users with point and click access to
traditionally command line driven tools written in R. We
demonstrate the ability to use MultiExperiment Viewer as a
graphical user interface for Bioconductor applications in
microarray data analysis by incorporating three Bioconductor
packages, RAMA, BRIDGE and iterativeBMA.

[Jari Häkkinen]

Added line breaks to the abstract.

[Nicklas Nordborg]

MeV+R seems to be a modified version of MeV. There are clearly R-related classes in mev-base.jar and mev-gui-impl.jar that are not present in the original MeV destribution. MeV+R is currently based on MeV 4.2 but our extension uses the official MeV 4.3. I guess if we want to do anything with MeV+R it must be done as a separate extension. The question is if MeV 4.2 is enabled for java web start.

[Nicklas Nordborg]

I made a quick check by replacing the JAR files from the regular MeV with the JAR files from MeV+R. It does start but the data file is not loaded. I guess this means that Java web start problems has been fixed in 4.2 but it still lacks support for command line parameters for loading files. I'll keep this ticket open in case MeV+R is updated with a new MeV version.

[Nicklas Nordborg]

The latest official MeV also has some R integration, but the R modules doesn't work when starting MeV from Java webstart. The main issue is that the R code is native to each platform and can't easily be distributed in the same way a Java program can. See "known issues" for the MeV 4.6 release at ​http://www.tm4.org/mev/features/releases