redmm | R Documentation |
'redmm' uses a feature matrix M from a random variable x and performs a singular value decomposition or Cholesky on M and creates a model matrix for x.
redmm(x, M = NULL, Lam=NULL, nPC=50, cholD=FALSE, returnLam=FALSE)
x |
as vector with values to form a model matrix or the matrix itself for an effect of interest. |
M |
a matrix of features explaining the levels of x. |
Lam |
a matrix of loadings in case is already available to avoid recomputing it. |
nPC |
number of principal components to keep from the matrix of loadings to form the model matrix. |
cholD |
should a Cholesky or a Singular value decomposition should be used. The default is the SVD. |
returnLam |
should the function return the loading matrix in addition to the incidence matrix. Default is FALSE. |
A list with 3 elements:
1) The model matrix to be used in the mixed modeling.
2) The reduced matrix of loadings (nPC columns).
3) The full matrix of loadings.
Giovanny Covarrubias-Pazaran
Covarrubias-Pazaran G (2016) Genome assisted prediction of quantitative traits using the R package sommer. PLoS ONE 11(6): doi:10.1371/journal.pone.0156744
The core functions of the package mmec
####=========================================####
#### For CRAN time limitations most lines in the
#### examples are silenced with one '#' mark,
#### remove them and run the examples
####=========================================####
data(DT_technow)
DT <- DT_technow
Md <- Md_technow
M <- tcrossprod(Md)
xx = with(DT, redmm(x=dent, M=M, nPC=10))
# ans <- mmec(GY~1,
# # new model matrix instead of dent
# random=~vsc(isc(xx$Z)),
# rcov=~units,
# data=DT)
# summary(ans)$varcomp
# u = xx$Lam * ans$uList[[1]] # change * for matrix product
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