View source: R/EMM_functions_cpp.R

EMM2.cpp | R Documentation |

This function solves single-kernel linear mixed model by EMMA (efficient mixed model association; Kang et al., 2008) approach.

```
EMM2.cpp(
y,
X = NULL,
ZETA,
eigen.G = NULL,
eigen.SGS = NULL,
tol = NULL,
optimizer = "nlminb",
traceInside = 0,
REML = TRUE,
bounds = c(1e-09, 1e+09),
SE = FALSE,
return.Hinv = FALSE
)
```

`y` |
A |

`X` |
A |

`ZETA` |
A list of variance (relationship) matrix (K; |

`eigen.G` |
A list with - $values
Eigen values - $vectors
Eigen vectors
The result of the eigen decompsition of |

`eigen.SGS` |
A list with - $values
Eigen values - $vectors
Eigen vectors
The result of the eigen decompsition of |

`tol` |
The tolerance for detecting linear dependencies in the columns of G = ZKZ'. Eigen vectors whose eigen values are less than "tol" argument will be omitted from results. If tol is NULL, top 'n' eigen values will be effective. |

`optimizer` |
The function used in the optimization process. We offer "optim", "optimx", and "nlminb" functions. |

`traceInside` |
Perform trace for the optimzation if traceInside >= 1, and this argument shows the frequency of reports. |

`REML` |
You can choose which method you will use, "REML" or "ML". If REML = TRUE, you will perform "REML", and if REML = FALSE, you will perform "ML". |

`bounds` |
Lower and Upper bounds of the parameter lambda. If the updated parameter goes out of this range, the parameter is reset to the value in this range. |

`SE` |
If TRUE, standard errors are calculated. |

`return.Hinv` |
If TRUE, the function returns the inverse of |

- $Vu
Estimator for

`\sigma^2_u`

- $Ve
Estimator for

`\sigma^2_e`

- $beta
BLUE(

`\beta`

)- $u
BLUP(

`u`

)- $LL
Maximized log-likelihood (full or restricted, depending on method)

- $beta.SE
Standard error for

`\beta`

(If SE = TRUE)- $u.SE
Standard error for

`u^*-u`

(If SE = TRUE)- $Hinv
The inverse of

`H = ZKZ' + \lambda I`

(If return.Hinv = TRUE)

Kang, H.M. et al. (2008) Efficient Control of Population Structure in Model Organism Association Mapping. Genetics. 178(3): 1709-1723.

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