Phase of Analysis

It is often a good idea to rerun an analysis for various reasons. Think of each run as a ``phase'' or step. For example, the first phase might be to identify QTL main effects. The second phase would then test the significance of each QTL just identified. The third phase might be to refine the positions of the remaining QTL and the fourth phase to estimate interactions. It is convenient to use the phase variable for this type of analysis. The phase variable, if set to an integer value greater than zero, will modify the names of the output file and the model input and output files. For a filename stem qtlcart and phase N, the output file will be qtlcartPhaseN.mim. The output model will be placed in qtlcartPhaseN.mqt, and the input model will be assumed to be qtlcartPhaseN-1.mqt. The phase variable is set with the -p option, and if greater than zero, will be incremented at the end of each successful run of MImapqtl.

Here is a sequence using the example dataset mletest.cro along with its map file mletest.map, both of which come with the programs. Assume that these two files have been placed in an empty subdirectory which is now the current working directory.

	% MImapqtl -A -V -I smprtSeC  -L 0.0 -S 1 -p 1 -X mletest &
	% MImapqtl -A -V -I sMPrTseC    &
	% MImapqtl -A -V -I sMPRtseC    &
	% MImapqtl -A -V -I sMPrtSeC    &
	% MImapqtl -A -V -I sMPrtsBC    &

The first invocation sets the filename stem, the information criterion and threshold for adding parameters and indicates that it is phase 1. The -I option tells MImapqtl to search for additive QTL. The second invocation tests each QTL found in the first phase. The third step refines the positions of all remaining QTL. The fourth step searches for more QTL (and probably won't find any). The fifth step searches for interactions between the identified putative QTL. The phase variable is updated after each step, so MImapqtl knows where to find the results from the previous step. The work code specified by the -I option is explained in the next section.