Is it possible to run a two part model for Scan1?

[Aravindh Nagarajan]

Hi Karl, 

I am working with data from CC mice, my phenotype has 0's for few lines. 

Is there a way to run a two part model in rqtl2 ?

- If i understand it correctly, use a binary model, for zero and one for all other values 

- Then, use the least squares for the non-zero values? 

Thank you, 

Aravindh

[Karl Broman]

It's not built in, but you can do a scan with a binary trait model, for a new trait defined by z=1 if y>0 and z=0 if y=0, and then a standard scan for a new trait where values with y=0 are replaced by NAs.

karl