BQTL - Bayesian Quantitative Trait Mapping

What's BQTL about?

Software for the mapping of genetic traits from line crosses and recombinant inbred lines is available here.

It performs

maximum likelihood estimation of multi-gene models
Bayesian estimation of multi-gene models via Laplace Approximations ( see paper )
interval mapping and composite interval mapping of genetic loci

It allows the user to

plot results
prepare printed reports
specify complicated, epistatic models using a flexible formula language
use covariates and specify interaction terms involving covariates and genetic effects

It consists of extensible modules written in S, C, and Fortran allowing the expert user to customize it to suit specific applications (e.g. non-standard crosses or phenotypic distributions). The software is engineered to work in conjunction with R (for UNIX, Linux, , Windows and MacOS)

R can be obtained from The Comprehensive R Archive Network R is freely available under the GNU Public License (see http://www.gnu.org/copyleft/gpl.html.) .

What platforms will BQTL run on?

Since BQTL uses R, it will run on any platform that supports R.

So, the short answer is: On Unix , Microsoft Windows (9x, NT, 2000), and MacOS.

Here is the long answer: R is implemented in a very portable fashion. Implementations exist for many Unix platforms including FreeBSD, NetBSD, Linux, Irix, Solaris, OSF/1, AIX and HPUX. In addition there are versions for Microsoft Windows (9x, NT, 2000) and for MacOS

How do I install BQTL so I can run it on my computer?

The same way you install any R package. This is outlined in the R FAQ. The latest version of the FAQ is available from http://cran.r-project/doc/FAQ/R-FAQ.html/ and there is a link to it on the CRAN mirror sites.

Follow the directions in the FAQ in the sections How can R be obtained?, How can R be installed?, and How can add-on packages be installed?

A Microsoft Windows binary version of BQTL is available on CRAN. You can use Packages menu in the RGui Windows version of R to install BQTL on a Windows system. See the R Windows FAQ for more details.

A simple sample of BQTL

### specify and run some models
data( little.ana.bc )	# read in pre-formatted data
little.lod <- bqtl( bc.phenotype ~ locus( all ) , little.ana.bc )	# ordinary interval mapping
plot( little.ana.bc, loglik(little.lod) )	# plot the interval map

### 20 models all involving marker 'm.12' and one of loci 31 thru 50
several.epi <- bqtl( bc.phenotype ~ m.12 * locus(31:50), little.ana.bc )	# epistasis with m.12
several.main <- bqtl( bc.phenotype ~ m.12 + locus(31:50), little.ana.bc )	# no epistasis
max.loglik <- max( loglik(several.epi) - loglik(several.main) )	# test the epistasis terms
print( max.loglik )

To get more details check out the bqtl function help pages

The current version of the R source code is available as a gzipped tar archive

Follow the usual instructions for installing from R package source on the CRAN Home Page

Scripts, Data, and Results from a QTL Mapping Project

The complete scripts, data, and results from the paper:

Quantitative Trait Loci Controlling Light and Hormone Response in Two Accessions of Arabidopsis thaliana.

by Borevitz JO, Maloof JN, Lutes J, Dabi T, Redfern JL, Trainer GT, Werner JD, Asami T, Berry CC, Weigel D, Chory J. Genetics. 2002 Feb;160(2):683-96.

are available as a zip archive.

The scripts implement the multigene models, genomewide scans for epistasis, and permutation tests reported in that paper.