-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2016-ddcb606466 2016-04-30 18:27:34.313635 --------------------------------------------------------------------------------

Name : R-qtl Product : Fedora 23 Version : 1.39.5 Release : 1.fc23 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/.

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 --------------------------------------------------------------------------------