Hypothesis tests

You need to set the hypothesis test for $SF_x$ and $RF_x$ crosses. The default of 1 is fine for crosses in which there are only two marker genotypic classes (backcrosses and recombinant inbreds). For $SF_x$ and $RF_x$, values of 30, 31 or 32 are valid. Recall that we have the following hypotheses:

1. $H_0: a = d = 0$
2. $H_1: a \neq 0 , d = 0$
3. $H_2: a = 0 , d \neq 0$
4. $H_3: a \neq 0, d \neq 0$

For 30, we test $H_3:H_0$. For 31, we test $H_3:H_0$, $H_3:H_1$ and $H_1:H_0$. For 32, we test $H_3:H_0$, $H_3:H_2$ and $H_2:H_0$. 30 is probably fine for initial scans.

Also, if you do only have two genotypic classes, then 10 is the same as 1 for the hypothesis test.