Fedora 21 Update: R-qtl-1.33.7-1.fc21

updates at fedoraproject.org updates at fedoraproject.org
Sat Nov 1 16:21:02 UTC 2014

Fedora Update Notification
2014-10-14 03:36:20

Name        : R-qtl
Product     : Fedora 21
Version     : 1.33.7
Release     : 1.fc21
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 1.33, 2014-08-12:

Major changes:
* Can read/write 4-way cross data in MapQTL format (thanks to Timothee Flutre).

Minor changes:
* read.cross with format="qtlcart" can now read doubled haploids (dh/Ri0).
* Fixed potential problem in read.cross with format="csv" or "csvs" when there are many empty cells in the phenotype data.
* Fixed bug in read.cross for format="csv" that shows up in some rare cases: markers not ordered by linkage group, no positions provided, and chromosome IDs non-numeric. It was a pretty bad bug, as marker genotypes got scrambled.
* Fixed some memory leaks in MQM code.


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/.

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