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GCTA `GREML` estimates were fitted as follows:
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|
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```{r eval = FALSE}
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gcta64 --reml-bivar 1 2 --grm-gz large.gcta --pheno large.gcta.phe
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--reml-bivar-lrt-rg 0 --thread-num 4 --out Y1_Y2 --reml-maxit 1000 >
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|
large.gcta.Y1Y2.log`
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```
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|
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which yielded the estimates:
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|
|
|
```{r eval = FALSE}
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Summary result of REML analysis (shortened output):
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|
Source Variance SE
|
|
|
V(G)/Vp_tr1 0.361387 0.020470
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|
V(G)/Vp_tr2 0.635426 0.015053
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|
rG 0.557367 0.026039
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|
```
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|
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|
Similar estimates can be obtained with `grmsem`, using a Cholesky model:
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|
|
|
|
```{r eval = FALSE}
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|
|
ph.biv<-ph[,c(1,2)]
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|
|
fit <- gsem.fit(ph.biv, G, LogL = TRUE, estSE = TRUE)
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|
|
print(fit)
|
|
|
st.fit <- gsem.stpar(fit)
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|
|
print(st.fit)
|
|
|
st.var.fit <- gsem.var(st.fit)
|
|
|
print(st.var.fit)
|
|
|
```
|
|
|
|
|
|
The standardised variances are (shortened output):
|
|
|
|
|
|
```{r eval = FALSE}
|
|
|
$VA
|
|
|
1 2
|
|
|
Y1 0.3613708 0.2669526
|
|
|
Y2 0.2669526 0.6349136
|
|
|
|
|
|
$VA.se
|
|
|
1 2
|
|
|
Y1 0.01943807 0.01555813
|
|
|
Y2 0.01555813 0.01355490
|
|
|
|
|
|
$RG
|
|
|
1 2
|
|
|
Y1 1.0000000 0.5573145
|
|
|
Y2 0.5573145 1.0000000
|
|
|
|
|
|
$RG.se
|
|
|
1 2
|
|
|
Y1 7.179876e-18 0.0239077
|
|
|
Y2 2.390770e-02 0.0000000
|
|
|
|
|
|
|
|
|
```
|
|
|
|
|
|
Both, GCTA and GSEM estimates from bivariate models, correspond to the GSEM estimates from the quad-variate Cholesky model (see above). |
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\ No newline at end of file |