Error in userGWAS

[saco...@colorado.edu]

Hello,

I was able to successfully run a user specified model without individual SNP effects, however when I try to run the same model in userGWAS I get the error:

object 'ReorderModel' not found 

I can't seem to find what could be causing this error or how to fix it. This is the model I am using, if it is of help:

testmodel <- 'F1 =~ NA*Trait1 + Trait2

             F2 =~ NA*Trait3 

             F3 =~ NA*Trait4 + Trait5         

             F1~~F3

             F2~~F3

             F1~~F2

             Trait3 ~~ 0*Trait3'

Thanks,

Sarah

[agro...@gmail.com]

Hi Sarah, 

Were you using the std.lv = TRUE command when running the user specified model? As written I don't believe your model is identified, and the std.lv argument isn't available for userGWAS, so I'm wondering if that is causing the error. It also doesn't look like you are including the effect of a SNP in that model which is likely causing additional issues. I might try rewriting the model as below, but you should confirm this actually matches your analytic question: 

testmodel <- 'F1 =~ NA*Trait1 + Trait2

             F2 =~ NA*Trait3 

             F3 =~ NA*Trait4 + Trait5         

             F1~~F3

             F2~~F3

             F1~~F2

             F1~~1*F1

            F2~~1*F2

            F3~~1*F3

           F1~SNP

          F2~SNP

          F3~SNP

             Trait3 ~~ 0*Trait3'

Best, 

-Andrew

[saco...@colorado.edu]

Hi Andrew,

Yes, I was using the std.lv = TRUE command. I also see now that I forgot to add the SNP effects. I will give those changes a try and see if it works. Thank you for your help!

Sarah