Analyzing real data

Create a new working subdirectory called realdat in you qwork subdirectory. Copy the realdat*.inp files into it. There should be two files: realdatm.inp and realdatc.inp. The former is a genetic linkage map in the standard input format (map.inp). The latter is a file with marker and trait data in the standard input format (cross.inp). This is a real data set kindly provided by Juan Medrano [Horvat and MedranoHorvat and Medrano1995]. It has also been used as an example in a review on the statistical issues in QTL mapping [Doerge, Zeng, and WeirDoerge et al.1997]. You will now translate the data files into the QTL Cartographer format, and then analyze the data.

1. Start up Rmap. Change the working subdirectory, and then the filename stem. You can use ``realdat'' for the stem. Now, select item 1 from the menu and enter realdatm.inp. Now run the program. Rmap should read in the prepared genetic linkage map file and reformat it properly.
2. Start up Rcross. Select item 1 from the menu and enter realdatc.inp. Now run the program. Rcross should read in the prepared data file, match marker names from this data file to those in the map file, and reformat the data properly. Look at the output.
3. Proceed with the analysis programs as in the previous examples. Run Qstats, LRmapqtl, SRmapqtl and Zmapqtl. Look at the output after each run.
4. Start up Preplot. Don't change any parameters: Go ahead with the program.
5. View the results using Gnuplot.
6. Start up Eqtl. Go ahead with the analysis. Look at the output (realdat.eqt).

Again we assume that QTLCartUnix/example is based in your home directory. The UNIX equivalents of the above are

% cd qwork
% mkdir realdat
% cd realdat
% cp ~/QTLCartUnix/example/realdat* .
% Rmap -A -i realdatm.inp -X realdat
% Rcross -A -i realdatc.inp
% Qstats -A  
% LRmapqtl -A
% SRmapqtl -A 
% Zmapqtl -A 
% Zmapqtl -A -M 6
% Preplot -A
% gnuplot mletest.plt
% Eqtl -A