Fedora 22 Update: R-qtl-1.38.4-1.fc22

[updates at fedoraproject.org]

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Fedora Update Notification
FEDORA-2016-32ddf9f96e
2016-02-20 20:26:17.666198
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Name        : R-qtl
Product     : Fedora 22
Version     : 1.38.4
Release     : 1.fc22
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 1.38, 2015-12-03  Major changes:  * Get rid of everything to do with
degrees of freedom in scanone and   scantwo. The checks seem to offer little
value but rather produce   cryptic warnings that confuse many users.  * Fixed a
bug in scanone() when using weights with multiple phenotypes   when some of the
phenotypes contain missing values.  Minor changes:  * In plotLodProfile, if col
has length > 1 but no equal to the number   of QTL, give a warning, but either
repeat or subset the vector   rather than just using the first value.  *
Modified read.cross with format "mm" to handle files with "bc" where   we
usually see "backcross".
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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 https://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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