gordonliu810822 / comm Goto Github PK

Hi

Nice method/package!
Will it be possible to add to the documentation details of the output values of the CoMM* functions? For CoMM_S4 I see the following values. Is alphag to be interpreted as the effect of gene expression on phenotype?
"vardist_mu" "sigma2mu" "alphag" "Lq" "LRLB"
Thanks

Hi,
Sorry for interrupting you. This is zhongshang Yuan. In source code CoMM_covar_pxem_ptr.cpp, the definition of the fucntion loglike_twas is confused with me.

Since the loglikelihood function are used for the LRT test, the loglike_twas fucntion should be the incomplete likelihood (i.e. the observed likelihood), which should integrate out the latent variable u from the expression (6). However, the definition in your code seems quite different.

Furthermore, the definition looks quite similar with the expression (9), However, the trace term in expression (9) has been missed and it is not equal to the term "sum(log(R.diag()))".

Would you like to explain this to me?

Thanks a lot. I am looking forward to your reply.