paper ~ symbolic computation code ~ figures

This page contains supplementary material for Sen S, Satagopan JM, Churchill GA (2005) "Quantitative trait locus study design from an information perspective," Genetics, 170:447-464. Please email me if you have any problems or questions about the contents of this webpage.

The code is basically unchanged from 2005 and recently uploaded onto this site.

Some of the results in the paper were derived using symbolic calculations in Maxima. Start Maxima in your system, and then you can cut and paste the contents of the files below into the command window. The files are commented, so you should be able to follow the steps.

• Formula for missing information in backcross: bc-missing.max
• Calculating the determinant and inverse of the information matrix for F2's: f2det.max
• Formula for missing information in backcross in the presence of a second QTL, assuming that first QTL has small effect: 2qtl.max

• Figure 1: genopat.m; this uses Pseudomarker version 0.9 written in Matlab, and the salt-induced hypertension data from Sugiyama et.al. (2001)
• Figure 2: chr4.R; this uses the R/qtl package
• Figure 3: numerical.R
• Figures 4 and 5: optimal.R
• Figure 6: opt-alpha.R; this uses the R/qtlDesign package version 0.32 (see below).
• Figure 7: replication.R
• Figure 8: 2qtl.R

This package performs power calculations and minimum effect size determinations for backcross and F2 intercross populations. These calculations take into account selective genotyping of the extreme phenotypic individuals and marker spacing. It is an add-on package to the R programming language. To install version 0.32 of the package (in UNIX or OS X) download the file qtlDesign_0.32.tar.gz, and give the type in a command window:

   R CMD INSTALL qtlDesign_0.32.tar.gz

For more recent versions of the package see the R/qtlDesign page on CRAN.