Change into the mr subdirectory. Run the following set of commands:
% JZmapqtl -A -V -X mletest -M 9 -I 10 % MultiRegress -A -V % Rqtl -A -V -i mletest.mr -o mletestPhase0.mqt % MImapqtl -A -V -I sMPrTseC -p 1 % MImapqtl -A -V -I sMPrtSeC
As in the previous example, compare the mletestPhase*.mqt files to the true model in mletest.qtl. The first is the model as estimated from multiple regression of the trait on genotypic expected values every two centimorgans. The second is a reduced model in which MImapqtl has deleted non-significant QTL. The third (mletestPhase2.mqt) contains a model after MImapqtl has searched for more QTL. Is this final model closer to the true model than the model obtained by de novo analysis? How long did this set of commands take?