Fedora 24 Update: R-qtl-1.39.5-1.fc24

updates at fedoraproject.org updates at fedoraproject.org
Tue Apr 19 20:33:54 UTC 2016

Fedora Update Notification
2016-04-19 20:29:26.932459

Name        : R-qtl
Product     : Fedora 24
Version     : 1.39.5
Release     : 1.fc24
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.

Update Information:

Version 1.39, 2016-03-04  Major changes:  * Fixed a bug in scantwo() when using
weights with multiple phenotypes   when some of the phenotypes contain missing
values. (This is the   same as the bug fix in scanone in version 1.38. Reminder
of   important principle: when you find a bug, look for other possible
instances of the same bug.)  * Changed the color scheme for plot.scantwo and
plot.rf from red/blue   rainbow to Viridis (see Option D at
https://bids.github.io/colormap/)   The plot.rf function has a new argument
col.scheme; if you want to   use the old red/blue scheme, use
col.scheme="redblue".  * Fixed a bug in cim() that was causing a segmentation
fault.  Minor changes:  * Added a function table2map() for converting a data
frame with marker   positions (chr, position) into a map object.  * Added a bit
more detail in the help file for readMWril().

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/.

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