qtl mapping from an information perspective

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 Saunak Sen(sen@biostat.ucsf.edu) if you have any problems or questions about the contents of this webpage.


The source code and software distributed in this web page has no implied warranty. Use at your own risk.

Symbolic computation code

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.
  • Figure 7: replication.R
  • Figure 8: 2qtl.R