Simulating and Analyzing data

Assuming that you have a qwork subdirectory (folder), create a new subdirectory (folder) within it. You can call it anything you like, but for the purposes of illustration it will be referred to as sim. Thus, your working directory for this example will be ::qwork:sim if on a Macintosh or ..$\backslash$qwork$\backslash$sim if on a PC. If you are on a UNIX machine, cd into the qwork/sim subdirectory and don't worry about setting a working subdirectory. Also note that if you are using a PC, the program names will all have an ``.exe'' ending, while for the Macintosh, you will double click the program icon.

In this exercise, you will simulate a genetic linkage map, then a model and finally a data set. This data will then be analyzed.

1. Start up Rmap. Select the option to change the filename stem. Change the filename stem to ``sim''. Now select the option to change the working directory and set it as suggested above. After this, you can change any parameters that you like. We suggest changing the variances of markers per chromosome and intermarker distance to values other than 0.0. In each case, a value of 2 or 3 would work well for the purposes of this exercise. Don't change the output format. When satisfied with the parameter values, select ``0'' to run the program. Look at the output (sim.map).
2. Start up Rqtl. You probably don't need to change any parameters. You can run this program with the ``0'' option. Look at the output (sim.qtl).
3. Start up Rcross. Again, you do not need to change any parameters, but you could try a different experimental design. Select the number associated with the experimental design. Change its value from ``B1'' to ``SF3'' (or whatever you like from Table 1.1). Run this program with the ``0'' option. Look at the output (sim.cro). From this point on, the analyses will utilize this file and the sim.map file.
4. Start up Qstats. and run it without changing any parameters. Look at the output (sim.qst).
5. Start up LRmapqtl and run it without changing any parameters. Look at the output (sim.lr).
6. Start up SRmapqtl. Run it and look at the output (sim.sr).
7. Start up Zmapqtl. You won't need to change any parameters. Tell it to go ahead with the analysis and look at the output (sim.z).
8. Start up Zmapqtlagain. This time, choose ``Model for Analysis'' and change it to ``6''. Tell it to go ahead with the analysis, and look at the output (which will be appended to what you did in the first run). Model 6 is composite interval mapping, and Zmapqtlwill use the ranked markers from the SRmapqtlrun to determine which cofactors to use.
9. Start up Preplot. Don't change any parameters: Go ahead with the program.
10. View the results using Gnuplot.
11. Start up Eqtl. Go ahead with the analysis. Look at the output (sim.eqt).

On a UNIX machine, the above can be accomplished with the following series of commands:

% mkdir qwork
% cd qwork
% mkdir sim
% cd sim
% Rmap -A -X sim -vm 2 -vd 3
% Rqtl -A
% Rcross -A  -c SF2
% Qstats -A
% LRmapqtl -A
% SRmapqtl -A 
% Zmapqtl -A 
% Zmapqtl -A -M 6
% Preplot -A
% gnuplot sim.plt
% Eqtl -A