Best-twopoints Documentation

3-20-97: A new twopoint analysis function was added: (best-twopoints). It requires three input items: the number of results to be shown, and two lists of marker numbers. For example: 
* (best-twopoints 4 '(0 1 2 3 4 5 6) '(7 8 9 10))

In this example, the twopoint lod score and recombination fraction will be computed for each marker in the first list versus each marker in the second list. They will then be ranked by lod score, and the pairs with the 4 highest lod scores will be printed to the screen. An example of the output can be seen here. This output was produced using the "chromosome 50" test set that is distributed with MultiMap. As with all MultiMap functions, it is necssary to first initialize MultiMap for your data set as follows: 

* (multimap 50 :run nil)

When working with large sets you may find it easier to use variables or additional functions to help in specifying your lists. For example, you could set a variable to hold your list, then use the variable name in the (best-twopoints) function instead of the actual list. In the following example, this series of commands produces the same results as the best-twopoints command above. The terms "lista" and "listb" are arbitrary and you can choose any name you like (provided you do not choose a LISP-reserved word). 

* (setf lista '(0 1 2 3 4 5 6))
* (setf listb '(7 8 9 10))
* (best-twopoints 4 lista listb)

Alternatively, you could use the (make-a-list) or (specify-list) functions to create the necessary lists. Detailed documentation on these is available here. It is important to read this documentation before using these functions. The following examples all produce the same analysis as the two examples of (best-twopoint) given above.