ProbABEL v0.4.0 released

The ProbABEL development teams is happy to announce the release of ProbABEL v0.4.0 after 8 months of development.

The most important user-visible changes are:
1) the output files now contain a column with chi2 values.
2) the CoxPH module is now fully functional again and can use filevector (DatABEL) files as well
3) for those of you who use probabel.pl: the way the -o option works has been slightly changed.

Thanks to all who made this release possible, by providing code, by being beta testers, by suggesting enhancements, or otherwise.

Below follows a more detailed break down of the changes since v0.3.0:

  • The output files now contain a chi2 column with the chi2 value based on the LRT when not using --mmscore. When using --mmscore, the chi2 values are calculated from the Wald statistic (not implemented for the 2df model yet).
  • Fixed long-standing bug #1130: The Cox regression module of ProbABEL crashes (when using filevector files). Actually, the Cox PH module was broken ever since ProbABEL v0.1-9e. Thanks to the Erasmus Medical Center, Rotterdam (the group of prof. C.M. van Duijn) and the Radboud University Medical Center, Nijmegen (the group of prof. Kiemeney) for partially sponsoring the time spent on this fix. Also thanks to Ben Verhaaren and Anne Grotenhuis for testing!
  • Fixed bug #2575: ProbABEL chooses weird file names if the -o option is not specified. As a result of this fix, usage of the -o option with probabel.pl is slightly changed. Before the string specified after -o was added to the name of the phenotype file. Now it indicated the complete start of the file name (as before model-dependant strings like _2df will be added automatically).
  • Fixed bug #2772: palogist with --mmscore crashes (memory issue). Thanks to Anuj Goel for reporting this bug.
  • Fixed bug #4700: wrong order of betas and se_betas in header of 2df output files. Thanks to Anne Grotenhuis for reporting this bug and to Yurii Aulchenko for solving it.
  • Fixed bug #4683: probabel.pl writes to the wrong directory if a relative path is given on the command line (Thanks to Aaron Isaacs for reporting this bug). NOTE: As a result of this fix giving the -o option to probabel.pl is no longer interpreted as an addition to the default prefix (which was the name of the phenotype file), but as a full file name (incl. path).
  • Fixed bug #2598: The prepare_data.R script is mentioned in the manual, but not distributed in the .deb or .tar.gz files
  • Fixed bug #2529: ProbABEL doesn't warn when a required file is not specified on the command line
  • Fix small bug where running palinear, palogist or pacoxph with the -h complained about a missing argument.
  • The examples directory has been cleaned up and the test suite has been moved to a separate directory.

More details of the bugs can be found on our R-forge bug tracker. This is also the place where you can inform us of new (or old) bugs.