G.predict {ASRgenomics} | R Documentation |

## Generates the conditional predictions of random effects (BLUPs)

### Description

Predicts random effects values for individuals with unobserved responses (here called `x`

,
a vector of length `nx`

) based on known random effect values for individuals with
observed responses (here called `y`

, a vector of length `ny`

). This is done using the
common genomic relationship matrix `\boldsymbol{G}`

for all
individuals (full matrix of dimension `(nx + ny) \times (nx + ny)`

).

The prediction of unobserved responses will be performed through the
multivariante Normal conditional distribution. These predictions are identical to
what would be obtained if the entire set of individuals (`nx + ny`

) were included into a
GBLUP animal model fit with individuals in the set `x`

coded as missing.

The user needs to provide the matrix `\boldsymbol{G}`

in full form.
Individual names (`nx + ny`

) should be assigned to `rownames`

and `colnames`

, and these
can be in any order. If the variance-covariance matrix of the set `y`

is provided,
standard errors of random effects in set `x`

are calculated.

### Usage

```
G.predict(G = NULL, gy = NULL, vcov.gy = NULL)
```

### Arguments

`G` |
Input of the genomic relationship matrix |

`gy` |
Input of random effects ( |

`vcov.gy` |
The variance-covariance matrix associated with the random effects from the
individuals with known values (set |

### Value

A data frame with the predicted random effect values for individuals with
unobserved responses in the set `x`

. If the variance-covariance matrix is provided,
standard errors are included in an additional column.

### Examples

```
## Not run:
library(asreml) # Load asreml.
# Example: Apple data creating 100 missing observations.
# Prepare G (nx + ny).
G <- G.matrix(M = geno.apple, method = "VanRaden", sparseform = FALSE)$G
dim(G)
# Prepare subset of data.
# Select only 147 from 247 individuals from pheno.apple and geno.apple.
Gy <- G[1:147, 1:147]
phenoy <- pheno.apple[1:147, ]
# Obtain the BLUPs for the 147 individuals using ASReml-R.
# Blend Gy.
Gyb <- G.tuneup(G = Gy, blend = TRUE, pblend = 0.02)$Gb
# Get the Gy inverse
Gyinv <- G.inverse(G = Gyb, sparseform = TRUE)$Ginv.sparse
# Fit a GBLUP model
phenoy$INDIV <- as.factor(phenoy$INDIV)
modelGBLUP <-
asreml(
fixed = JUI_MOT ~ 1,
random = ~vm(INDIV, Gyinv),
workspace = 128e06,
data = phenoy)
# Obtain Predictions - BLUP (set y).
BLUP <- summary(modelGBLUP,coef = TRUE)$coef.random
head(BLUP)
gy <- as.matrix(BLUP[, 1])
rownames(gy) <- phenoy$INDIV
# Ready to make conditional predictions.
g.cond <- G.predict(G = G, gy = gy)
head(g.cond)
## End(Not run)
```

*ASRgenomics*version 1.1.4 Index]