ProbABEL v0.5.0 released

Almost one year after the release of v0.4.5, the ProbABEL development team is happy to announce the release of v0.5.0.
This release contains several important improvements and fixes and all users are encouraged to upgrade.

(Please click on "read more", below, for more details.)

Information on how to get the source code or binaries can be found on the ProbABEL page. Please note that since most people (if they use Windows for this type of analysis at all) run 64 bit Windows, we stopped providing 32 bit binaries.

The most important user-visible changes are:

  1. ProbABEL now depends on the Eigen library for fast matrix algebra. Eigen v3.2.1 is included in the ProbABEL source package, so this should be transparent for the user.
  2. palinear, palogist and pacoxph have a new option: --flipmaf. If this option is selected, ProbABEL will 'flip' the alleles A1 and A2 for those variants for which the Freq1 value in the info file is less than 0.5. Changing the reference and effect allele in this way can sometimes (for some genetic models and low MAF), reduce regression errors and thus result in proper estimates which otherwise be set to NaN. Many thanks for the group of Prof. Kiemeney at the dept. for Health Evidence Radboud UMC in Nijmegen (NL) for sponsoring the work on this feature! Also thanks to Tessel Galesloot from the same group for extensive testing of this release.
    This also fixes issue #5.
  3. Several speedups were implements. For example, linear regression with mmscore is 2 times faster, reading of mldose/mlprob files is 14 times faster. Overall the runtime for linear regression is now about 5 times faster. Thanks to Maarten Kooyman!
  4. Fixed issue #15: "Coxph interactions are not working; when using the --interaction option the incorrect was used.
  5. Fixed issue #16: "Too many NANs for SNPs with low `Rsq` when some command line options are specified".
  6. Fixed issue #21: The obsolete --interaction_only option has been removed. Thanks to Matthias Wuttke for reminding us of this bug.
  7. Fixed bugs #5883 & #6010 (on R-forge): The main effect is displayed in the output with the `interaction_only` option. Thanks to Maksim Struchalin & Lennart Karssen for fixing it and to Farid Radmanesh for reporting it. This was only a display error, computations were not affected.

For a full list of changes, see the doc/ChangeLog file.

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

For support, please go to the ProbABEL section of the forum. Bugs can be reported in the bug tracker.