GenABEL announcements

Questions about GenABEL (aka *ABEL) suite of packages
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GenABEL announcements

Postby admin » Tue Jan 04, 2011 3:10 pm

In this sticky topic announcements about GenABEL will be made. New versions will be announced here.

yurii
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GenABEL v. 1.6-5

Postby yurii » Tue Feb 08, 2011 3:53 pm

GenABEL v. 1.6-5 is on CRAN. Enjoy!

New functions and features
  • New Fan's & Maksim's compound heterozygosity association test added, can be called through two names (chi2_CG == cocohet)
  • Added mechanism to check for the (latest) version at load time

Fixes and updates
  • Moved summary.snp.data to 'iterator' framework, changes in gwaa.data@gtdata@gtps definition, now 'ANY' allowing for use of different types of data with "interator". Interestingly, for 'old' data type computations became faster!
  • Added extra checks for impute2databel to ensure that sample file header is not used
  • Change in merge.snp.data by Maksim Struchalin, adding option "intersected_snps_only" (if TRUE, then only interesected SNPs will be in output)
  • Disabled check on intermediateXF in check.marker by setting intermediateXF=c(.5,.5) by default. This will be dealt with further (see tracker '[#1210] intermediate inbreeding checks with check.marker' )
  • polygenic() added default option patchBasedOnFGLS, if no convergence based on difFGLS criterion, fixed effect betas are patched to FGLS betas before starting re-iteration
  • Fixed 'demo(ge03d2)'
  • 'stepids' argument added to export.merlin
  • Bug fix in export.plink() thanks to Nadya Belonogova
  • Made sure that SE reported does not carry the sign of beta (always 'abs')

For more details, see CHANGES.LOG at https://r-forge.r-project.org/scm/viewv ... ot=genabel

yurii
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New R package 'PredictABEL' available on CRAN!

Postby yurii » Fri Feb 11, 2011 2:10 am

PredictABEL, a GenABEL-family R package for assessing the performance of risk models for binary outcomes, is available from CRAN, http://cran.at.r-project.org/web/packag ... index.html

PredictABEL includes functions to assess the performance of risk models. The package contains functions for the various measures that are used in empirical studies, including univariate and multivariate odds ratios (OR) of the predictors, the c-statistic (or area under the receiver operating characteristic (ROC) curve (AUC)), Hosmer-Lemeshow goodness of fit test, reclassification table, net reclassification improvement (NRI) and integrated discrimination improvement (IDI). Also included are functions to create plots, such as risk distributions, ROC curves, calibration plot, discrimination box plot and predictiveness curves. In addition to functions to assess the performance of risk models, the package includes functions to obtain weighted and unweighted risk scores as well as predicted risks using logistic regression analysis. These logistic regression functions are specifically written for models that include genetic variables, but they can also be applied to models that are based on non-genetic risk factors only.

Many thanks to Suman Kundu, Cecile Janssens, and Lennart Karssen for doing great job!

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New ProbABEL release

Postby lckarssen » Sun May 15, 2011 9:40 pm

A new release of the ProbABEL 0.1-9e source code can be found here and on the GenABEL website.

This release fixes an issue that made it impossible to compile the code (see this forum post and the bug report).
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Lennart Karssen
PolyOmica
The Netherlands
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yurii
GenABEL developer
GenABEL developer
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GenABEL package v. 1.6-7

Postby yurii » Sat Jun 18, 2011 5:04 pm

GenABEL package is 1.6-7 is now considered current stable release.

This release contains a number of new functions and bug fixes. The package is available from CRAN.

For more details, please visit http://www.genabel.org/news20110618

yurii
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GenABEL developer
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Journal Club opened

Postby yurii » Tue Jul 12, 2011 9:52 pm

A new forum “Journal Club on Statistical Genomics” was started within the GenABEL project. This forum is supposed to bring together the curious questions and smart answers on statistical genomics based on the on-line open access bibliography. Read more at http://www.genabel.org/news20110712
Note that (Gen)ABELs are dynamically developing; while this post is intended to provide full information at the time of posting, please read on further posts, if any, as the topic may be updated with novel solutions at a later stage.

best regards,
Yurii

lckarssen
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Re: GenABEL announcements

Postby lckarssen » Thu Oct 20, 2011 12:46 pm

Suman Kundu has released version 1.2 of the PredictABEL package on CRAN. The most important changes are:
  • Add the function, simulatedDataset, to construct a simulated dataset that contains individual genotype data, genetic risk, and disease status, which is used for the evaluation of genetic risk models.
  • Modify the function reclassification to include any number of cut-off values.
  • Modify the function plotDiscriminationBox, which can include any continuous measures (risk scores/ predicted risks) to create box plots for cases and controls.
-------
Lennart Karssen
PolyOmica
The Netherlands
-------

yurii
GenABEL developer
GenABEL developer
Posts: 263
Joined: Fri Jan 21, 2011 5:20 pm

GenABEL package v. 1.7-2

Postby yurii » Wed Sep 19, 2012 10:04 am

GenABEL package v. 1.7-2 (stable) is released on CRAN.

This version features several smaller updates, and also new implementation of the 'grammar' function, including Grammar-Gamma method.

For more information, see abou the release, see http://www.genabel.org/news20120919. For more information about Grammar-Gamma, see http://www.genabel.org/news20120917.
Note that (Gen)ABELs are dynamically developing; while this post is intended to provide full information at the time of posting, please read on further posts, if any, as the topic may be updated with novel solutions at a later stage.

best regards,
Yurii

lckarssen
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Re: GenABEL announcements

Postby lckarssen » Mon Aug 12, 2013 7:23 am

We have set up a mailing list specifically for announcements of new packages in the GenABEL project as well as updates to the existing projects.
So if you would like to get an e-mail when GenABEL packages are updated, please subscribe to the genabel-announce list at our R-forge site.
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Lennart Karssen
PolyOmica
The Netherlands
-------

lckarssen
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Re: GenABEL announcements

Postby lckarssen » Thu Sep 11, 2014 9:23 am

A new version of DatABEL has just been published on CRAN. Thanks to Maksim Struchalin for uploading the package!

The most important changes in DatABEL v0.9-5 are two fixed bugs:
- Fixed bug #5793: impute2DatABEL gives several errors
- Fixed bug #1126: Using mach2databel() or impute2mach() to convert files to the filevector format leaves fvtmp files behind

Thanks to all who contributed to this release!
If you find any bugs, please report them in our bug tracker on R-Forge.
-------
Lennart Karssen
PolyOmica
The Netherlands
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