ProbABEL announcements

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lckarssen
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ProbABEL announcements

Postby lckarssen » Mon Jun 11, 2012 7:55 pm

In this sticky topic announcements about ProbABEL will be made. New versions will be announced here.
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ProbABEL v0.2.0 is out!

Postby lckarssen » Mon Jun 11, 2012 8:29 pm

It has been more than a year since the last ProbABEL release. Therefore, I am happy to announce a new release of ProbABEL: version 0.2.0 is out!

The most important changes:
  • pacoxph (for the Cox proportional hazards model) is no longer built by default, because it is too buggy at the moment (actually, that was already the case in the previous release...). We are working on fixing this. See the files doc/CHANGES.LOG and doc/INSTALL on how to compile pacoxph if you really want to.
  • Bug #1889 fixed: in palinear with mmscore the inverse variance-covariance matrix was not passed correctly resulting in wrong effect estimates (especially when only a few SNPs are used). Unfortunately, the present fix results in an increase in compute time of approximately 20% :(.
  • Experimental new feature: ProbABEL can analyse binary traits accounting for relationship structure. This adds the '--mmscore' option for logistic regression. See the ProbABEL manual for more details.
  • For those installing ProbABEL from source: ProbABEL now uses autoconf and automake so the regular

    Code: Select all

    ./configure
    make
    make check
    make install

    now work. See the file doc/INSTALL for more details.
  • The config file for probabel.pl will now be stored in /usr/local/etc by default.
  • Smaller changes:
    • Memory leaks fixed (Bug #1890)
    • Many improvements to the code layout and some small improvements to make ProbABEL compile with the -Wall option without too many warnings.
    • We now have man pages for pacoxph, palogist and palinear
Were to get it:
  • The source package can be found on the GenABEL website at: http://www.genabel.org/packages/ProbABEL
  • Users of Ubuntu (or one of its derivative distributions like Kubuntu or Linux Mint) can install the latest ProbABEL release from the GenABEL PPA (Personal Package Archive) by following these steps:

    Code: Select all

    sudo add-apt-repository ppa:l.c.karssen/genabel-ppa
    sudo apt-get update
    sudo apt-get install probabel
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Bug fix in ProbABEL's Cox PH module released

Postby lckarssen » Wed Aug 29, 2012 7:19 am

We are pleased to announce the release of ProbABEL v.0.1-3-pacoxph-fix-1. This release fixes bug #1846 (different results from the Cox PH module depending on whether genotype dosages or probabilities are used) in the older ProbABEL v.0.1-3. The fix of this bug was sponsored by the Radboud University Medical Centre, Nijmegen, The Netherlands (Prof. Kiemeney's group). We thank them for their financial support as well as for reporting the bug and their help in the follow-up that lead to the fix (with special thanks to Anne Grotenhuis). The copyright of the code of the fix is theirs, and they have agreed to release it under the GPL. We greatly appreciate the Radboud's contribution to the GenABEL project in particular and to free software in general. The source code can be downloaded from http://www.genabel.org/packages/ProbABEL/. Questions are welcome in the ProbABEL section of this forum.

Note that this code belongs to the branch ProbABEL/pacoxph, which does not support filevector/DatABEL data format yet (this branch is based on the older v.0.1-3 code). We are in the process of fixing the Cox module in the newer versions of ProbABEL, however, this will take some more effort. Any help is, of course, greatly appreciated.
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ProbABEL v0.2.2 has been released

Postby lckarssen » Tue Nov 06, 2012 11:36 pm

We are happy to announce a new release of ProbABEL: version 0.2.2 is out!
This version is an incremental update of v0.2.0, featuring several bug fixes and some new functionality in the probabel.pl script.

New functionality:
* Update of the probabel.pl script and probabel_config.cfg. The .cfg file now accepts the chr separator in multiple locations in the path (thanks to Marijn Verkerk). probabel.pl can now also run Y chromosome analysis and the help message has been updated.
* probabel.pl and probabel_config.cfg now also accept chunks, where dose, prob, info and map files are split into multiple chunks. This is now the default for people following the 1000 genomes imputation cookbook for MaCH/minimac (the recipe uses the chunkchromosome tool to split the data into smaller pieces, speeding up imputation on computer clusters). See probabel_config.cfg.example for an example.

Bugs fixed in this release:
* Fixed bug #2295: the inverse variance-covariance matrix (used with the --mmscore option) was incorrectly subsetted when NAs are present for one or more SNP dosages (so this is not an issue for people using imputed data). As a result the invvarmatrix that was actually used in the regression contained rows and columns of zeroes. Thanks to Maarten Kooyman for reporting this bug.
* Fixed bug #1186: When .map file is missing (but --map option was given), the wrong error message was displayed. Thanks to Nicola Pirastu for reporting this bug.
*Fixed bug #2147: The value of the Rsq column in the info file should be > 0, unlike what was mentioned in the documentation.

Were to get it:
* The source package can be found on the GenABEL website at: http://www.genabel.org/packages/ProbABEL
* Users of Ubuntu (or one of its derivative distributions like Kubuntu or Linux Mint) can install the latest ProbABEL release from the GenABEL PPA (Personal Package Archive) by following these steps:

Code: Select all

sudo add-apt-repository ppa:l.c.karssen/genabel-ppa
sudo apt-get update
sudo apt-get install probabel


Support:
For user support, you are at the right place. Bugs can be reported in our bug tracker on r-forge.
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ProbABEL v0.3.0 released

Postby lckarssen » Tue Jan 01, 2013 11:47 pm

With the new year comes good news: ProbABEL v0.3.0 has been released today.

This release marks the end of a lot of work done on the internals of ProbABEL, which was started earlier this year by Maarten Kooyman. The most important thing a user will notice is an approximately four-fold speed increase when running palinear with the --mmscore option as well as possible speed increases in other use cases as well.
In his e-mail to the development mailing list of 2012-12-21 Maarten explains his work in more detail, including a few graphs of the speed gains.

Major bugs fixed in this release:
  • Fixed bug #2436: probabel.pl doesn't overwrite output file (as it used to do before 0.2.2). This bug was introduced with the possibility of using SNP dosages/probabilities that are split into (sub-chromosomal) chunks.
Were to get it:
Support:
For user support, please take a look at our forums at http://forum.genabel.org. Bugs can be reported in our bug tracker on r-forge.
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ProbABEL v0.4.0 has been released

Postby lckarssen » Sun Aug 25, 2013 10:45 pm

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 chi^2 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.

The latest source code can be downloaded from http://www.genabel.org/packages/ProbABEL. Packages for Ubuntu will appear in the GenABEL PPA at https://launchpad.net/~l.c.karssen/+archive/genabel-ppa shortly.


Below follows a more detailed break down of the changes since v0.3.0:
  • The output files now contain a chi^2 column with the chi^2 value based on the LRT when not using --mmscore. When using --mmscore, the chi^2 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.
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Re: ProbABEL announcements

Postby lckarssen » Mon Sep 02, 2013 7:38 am

Shortly after the introduction of ProbABEL v0.4.0 a small bug was discovered when running with the --mmscore option. This release fixes that bug. The source code and more information can be found on the ProbABEL page.

A more detailed description ofthe bug can be found in the bug tacker.

Thanks to the Erasmus MC, Rotterdam for sponsoring this release.
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ProbABEL v0.4.2 released

Postby lckarssen » Thu Jan 02, 2014 1:58 am

The ProbABEL development teams is happy to announce the release of ProbABEL v0.4.2. Information on how to get the source code or binaries can be found on the ProbABEL page (http://www.genabel.org/packages/ProbABEL).

The most important user-visible changes are:
1) Starting with this release the probabel.pl wrapper script has been renamed to probabel. In order not to disrupt any current pipelines a symbolic link is created to the old name. When the user invokes the script with the old name a warning will be printed to encourage them to use the new name. The old name will remain available for several future releases, but will be removed at some point.
2) Improved convergence checks for the Cox PH regression module
3) Fixed a bug where ProbABEL crashed when having large indels in the
info file

For more information, please check the release announcement at http://www.genabel.org/node/287. Please submit bug reports to our bug tracker on R-forge.
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Re: ProbABEL announcements

Postby lckarssen » Wed Apr 02, 2014 7:35 am

Dear GenABEL users,

The ProbABEL development team is happy to announce the release of ProbABEL v0.4.3. This release is a minor update, mostly speeding up reading filevector data.
Information on how to get the source code or binaries can be found on the ProbABEL page.

The changes in this release are:
  • Speed-up of a factor of ~ 2 for linear, logistic and Cox regression when using input files in filevector format.
  • Improved documentation on the installation procedure in the ProbABEL manual (fixes bug #5403).
  • Fixed bug #5404: "ProbABEL's R check for Cox regression doesn't check if the survival package is installed".

Please use the forum for any questions you may have. Bugs and feature requests can be reported on our R-forge site.
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ProbABEL v0.4.5 released

Postby lckarssen » Wed May 27, 2015 9:34 pm

Dear users,

On behalf of those who contributed I am happy to announce the release of ProbABEL v0.4.5. This is a bugfix release fixing one serious bug in the Cox regression module, as well as several other bugs of lesser importance (also in the Cox module). Users of pacoxph are strongly advised to upgrade. For users of the linear and logistic modules nothing has changed.

Please read the full announcement on the GenABEL website. The tar-ball with the source code can be found ProbABEL web page.
Updated Debian and Ubuntu packages will be released shortly.

Special thanks go to the people who have contributed to this release by sending extensive bug reports via e-mail and the forum, as well as testing the fixes: forum user 'quentin300' and Anne Grotenhuis, thank you for your efforts!

Bugs and feature requests can be reported via our trackers on R-forge.
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