Which Results?

The output file from Zmapqtl may contain the results of analyzing different traits using different models. Furthermore, in $F_2$ and other populations in which dominance can be estimated, it is possible to test different sets of hypotheses. The user can specify which results from the Zmapqtl output file to process. The -M option tells Eqtl to examine the results from using the specified analysis model. An integer value should be given after the -M option. By default, Eqtl looks for the results from Model 3, or interval mapping. If you have done composite interval mapping, with say model 6, then you should specify -M 6 on the command line (or in the interactive menu). If model 6 was the last model run in Zmapqtl, then Eqtl should already be aware of that fact.

For $F_2$ design experiments (and others where there are three genotypic classes), various hypothesis tests can be performed. Recall that there are four hypotheses $H_0$, $H_1$, $H_2$ and $H_3$ that are explained in Section 3.4.4. Using -H with 10, 20, 30, 31 or 32 allows you to specify which likelihood ratio should be the basis for declaring QTL. Table 4.2 summarizes the output for various values used with the -H option.

Table 4.2: Output for different -H values with Eqtl

-H	Likelihood Ratio	$a$	$d$	$S$	$r^2, r_t^2$
10, 14	$H_1:H_0$	$a_1$	-	$S_1$	$H_1:H_0$
20	$H_2:H_0$	-	$d_2$	$S_2$	$H_2:H_0$
30, 34	$H_3:H_0$	$a_3$	$d_3$	$S_3$	$H_3:H_0$
31	$H_3:H_1$	$a_3$	$d_3$	$S_3$	$H_3:H_0$
32	$H_3:H_2$	$a_3$	$d_3$	$S_3$	$H_3:H_0$

Eqtl can process the results of running permutations, bootstraps and jackknives as well as of JZmapqtl. By default, Eqtl will only try to process the output of Zmapqtl and JZmapqtl. To change what Eqtl tries to process, use the -I option with a work code. This option takes a string as an argument, and each letter in the string tells Eqtl to do something. The default string is ZM, which indicates to process the single trait (Zmapqtl) and multi-trait (JZmapqtl) output. The letters PBJ tell Eqtl to process the permutation test, bootstrap and jacknife analysis files as well. Any combination of PBJZM may be used as the work code, but if P is to be used, then put it first because order of processing is the same as the order of the letters.