Multiple Interval Mapping

This section is generally done during the QTL II module at the Summer Institute in Statistical Genetics. This lab will usually start with a twenty minute introduction by the instructor. Since the first part of the exercise takes about twenty minutes to run, it is a good idea to start it before, and let it run during, the introductory lecture.

We will work with the files mletest.map and mletest.cro for this section. We are going to analyze the data in three ways. The first will be to use MImapqtl to find a model de novo. Then, we will use composite interval mapping to find an initial model for multiple interval mapping. Finally, we will use stepwise regression to determine an initial model and multiple interval mapping to complete the analysis.

Create a new subdirectory called mletest2 in your qwork subdirectory. Within that subdirectory, create three new subdirectories called ci, mi and mr. Place copies of the data files (mletest.map and mletest.cro) in each of these directories. In UNIX, you would do this:

% cd qwork
% mkdir mletest2
% cd mletest2
% mkdir ci
% mkdir mi
% mkdir mr
% cp ~/QTLCartUnix/example/mletest.* ci
% cp ~/QTLCartUnix/example/mletest.* mi
% cp ~/QTLCartUnix/example/mletest.* mr