Fedora 20 Update: R-qtl-1.36.6-1.fc20

[updates at fedoraproject.org]

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Fedora Update Notification
FEDORA-2015-3354
2015-03-09 04:34:45
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Name        : R-qtl
Product     : Fedora 20
Version     : 1.36.6
Release     : 1.fc20
URL         : http://www.rqtl.org/
Summary     : Tools for analyzing QTL experiments
Description :
R-qtl is an extensible, interactive environment for mapping
quantitative trait loci (QTLs) in experimental crosses. Our goal is to
make complex QTL mapping methods widely accessible and allow users to
focus on modeling rather than computing.

A key component of computational methods for QTL mapping is the hidden
Markov model (HMM) technology for dealing with missing genotype
data. We have implemented the main HMM algorithms, with allowance for
the presence of genotyping errors, for backcrosses, intercrosses, and
phase-known four-way crosses.

The current version of R-qtl includes facilities for estimating
genetic maps, identifying genotyping errors, and performing single-QTL
genome scans and two-QTL, two-dimensional genome scans, by interval
mapping (with the EM algorithm), Haley-Knott regression, and multiple
imputation. All of this may be done in the presence of covariates
(such as sex, age or treatment). One may also fit higher-order QTL
models by multiple imputation and Haley-Knott regression.

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Update Information:

Version 1.36, 2015-03-05

Major changes:
* None.

Minor changes:
* Added a function flip.order() for flipping the order of markers on selected chromosomes.
* Added scanonevar.meanperm and scanonevar.varperm (from Robert Corty) for permutation tests with scanonevar().
* Revised plotPheno (aka plot.pheno) so that one can control the x-axis label and title (also, in a histogram, the breaks).
* plotPXG: if infer=FALSE and there are no fully-informative genotypes (e.g., in a 4-way cross), give a more informative error.
* geno.image: allow control of x- and y-axis labels; allow suppression of axes.
* Removed some warnings about missing end-of-line characters, in read.cross with MapQTL format.
* Fixed a bug in scanonevar; was failing with an error about coercing class "A" to a data.frame
* Dropped the name summary.scantwo.old(); still available as summaryScantwoOld().

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ChangeLog:

* Fri Mar  6 2015 Mattias Ellert <mattias.ellert at fysast.uu.se> - 1.36.6-1
- Update to 1.36.6
* Sun Jan  4 2015 Mattias Ellert <mattias.ellert at fysast.uu.se> - 1.35.3-1
- Update to 1.35.3
* Mon Oct 13 2014 Mattias Ellert <mattias.ellert at fysast.uu.se> - 1.33.7-1
- Update to 1.33.7
* Fri Aug 15 2014 Fedora Release Engineering <rel-eng at lists.fedoraproject.org> - 1.32.10-5
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild
* Thu Jul 17 2014 Mattias Ellert <mattias.ellert at fysast.uu.se> - 1.32.10-4
- Remove stack limit workaround (bug fixed in R 3.1.1)
* Tue Jul  1 2014 Jakub Čajka <jcajka at redhat.com> - 1.32.10-3
- Changed stack limit on ppc64 and s390x to allow checks to pass
* Sat Jun 28 2014 Mattias Ellert <mattias.ellert at fysast.uu.se> - 1.32.10-2
- Disable checks on ppc64
* Wed Jun 25 2014 Mattias Ellert <mattias.ellert at fysast.uu.se> - 1.32.10-1
- Update to 1.32.10
- Use R-core-devel instead of R-devel as BR
- Re-enable checks
* Fri Jun  6 2014 Fedora Release Engineering <rel-eng at lists.fedoraproject.org> - 1.31.9-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild
* Thu May  8 2014 Tom Callaway <spot at fedoraproject.org> - 1.31.9-1
- Update to 1.31.9
* Sat Dec 21 2013 Mattias Ellert <mattias.ellert at fysast.uu.se> - 1.29.2-1
- Update to 1.29.2
- Add BR for blas-devel and lapack-devel
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This update can be installed with the "yum" update program.  Use
su -c 'yum update R-qtl' at the command line.
For more information, refer to "Managing Software with yum",
available at http://docs.fedoraproject.org/yum/.

All packages are signed with the Fedora Project GPG key.  More details on the
GPG keys used by the Fedora Project can be found at
https://fedoraproject.org/keys
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