The Work Code must be specified with an 8 letter string. Each letter in the string is a flag to tell the program whether to do a certain step. Some of the flags have options to modify the behavior of that step. The 8 letter string starts from position 0. The remaining positions (17) correspond to the steps given in the previous section.
This can take on values S or s. If S, then MImapqtl will go into scan mode. It will do one pass in the search for QTL phase, and print out positions and a likelihood profile to the output file. The user can then plot the values and decide where to place a new QTL.
Tells MImapqtl whether to use the initial model specified with the -E option. If M, then use the model, and if m, don't use it. If you use m, then you should also specify prt in positions 2, 3 and 4. For example, smprtSEC would make sense: It would search for QTL de novo.
Use a P here if you want MImapqtl to re-estimate the paramters in the initial model. Use a p if you want to skip this step. The case of this position should almost always match that of position 1.
Use an R here if you want MImapqtl to refine the position estimates in the initial model. Use an r if you want to skip this step. If you don't have an initial model, then this should be r. You can also extend the refinement of position to the immediate adjacent intervals by using A in this position.
Use a T here if you want MImapqtl to test the significance of the parameters in the initial model. Use a t if you want to skip this step. If you don't have an initial model, then this should be t. You can use D in place of T in order to test dominance effects only, but t his is only relevant with three marker classes. Finally, if you want to test any existing epistatic interactions, then use E.
Use an S here if you want MImapqtl to search for more QTL. Use an s if you want to skip this step. You can also specify a A if you only want to search for the additive effects of putative QTL (that is, don't search for dominance effects in Fx lines). Finally, if you use a D here, MImapqtl will only search for dominance effects at QTL locations that don't already have them.
Use an E here if you want MImapqtl to search for epistatic effects. Use an e if you want to skip this step. By default, the MImapqtl does a forward stepwise search for epistatic terms. If you want to try a backward elimination approach, use a B in this position, but be aware that if there are too many epistatic terms, the request will be ignored in favor of a forward search. Finally, a U in this postion will do a backward elimination approach but the limit to the number of parameters will be the sample size minus one.
Use a C here if you want MImapqtl to calculate the variance-covariance matrix, R2 values and breeding values for the final model. Use a c if you want to skip this step. If you specify an R in this spot, then for the current model, the residuals for the trait being analyzed are calculated and used as the new trait values. These residuals are written to a file stem.res where stem is the filename stem.
The default string is smprtSeC, which tells MImapqtl to scan for QTL without an initial model, where the the additive and dominance effects are treated as a unit.