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GNU R package for genetic marker linkage analysis

R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTLs) in experimental crosses. It is implemented as an add-on-package for the freely available and widely used statistical language/software R (see

The development of this software as an add-on to R allows to take advantage of the basic mathematical and statistical functions, and powerful graphics capabilities, that are provided with R. Further, the user will benefit by the seamless integration of the QTL mapping software into a general statistical analysis program. The 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.

Package version:1.16-6-2


README file for the qtl package
This explains the installation of the qtl package for R.  If you have
any problems with installation, send an email to Karl Broman


  You can download R from the Comprehensive R Archiv


Sample data for the R/qtl package

These files contain sample data in several formats, so that the user
may better understand how data may be formatted for import via the
read.cross function.  These are the same as the "listeria" data
set included with the R/qtl package.  

Note: Replace the "..." in the directory string to the appropriate
location of the sampledata directory (for example,


README.Debian for r-cran-qtl:

When using the package, please cite
	Broman KW, Wu H, Sen S, Churchill GA (2003)
	R/qtl: QTL mapping in experimental crosses.
	Bioinformatics  19:889-890 
in your publications.

Notes on how this package can be tested.


qtl (1.16-6-2) unstable; urgency=low

  * Added myself to Uploaders
  * Debhelper 7
  * Moved from p


"To do" list for R/qtl


This is the Debian GNU/Linux r-cran-qtl package of r/qtl, 
performing statistical analyses of genomi


Bugs and bug fixes for R/qtl

Browse inside r-cran-qtl_1.16-6-2_i386.deb

         [DIR]DEBIAN/ (2)  65535+ mirrors
         [DIR]usr/ (2)  65535+ mirrors

Download r-cran-qtl_1.16-6-2_i386.deb

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