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mxGREMLDataHandler
"phenotypes" actually represent multiple observations on the same variable. One
example of the latter case is longitudinal data where the multiple "phenotypes"
are repeated measures on a single phenotype.
Details
For a monophenotype analysis (only), argument Xdata can be a character vector. In a polyphenotype analysis, if the same covariates are to be used with all phenotypes, then Xdata can be a list of
length 1.
Note the synergy between the output of mxGREMLDataHandler() and arguments dataset.is.yX
and casesToDropFromV to mxExpectationGREML().
If the dataframe or matrix supplied for argument data has n rows, and argument yvars is of length
p, then the resulting ’y’ and ’X’ matrices will have np rows. Then, if either matrix contains any NA’s,
the rows containing the NA’s are trimmed from both ’X’ and ’y’ before being returned in the output
(in which case they will obviously have fewer than np rows). Function mxGREMLDataHandler()
reports which rows of the full-size ’X’ and ’y’ were trimmed out due to missing observations.
These row indices can be provided as argument casesToDropFromV to mxExpectationGREML().
Value
A list with these two components:
yX
Numeric matrix. The first column is the phenotype vector, ’y,’ while the remaining columns constitutethe ’X’ matrix of covariates. If this matrix is used
as the raw dataset for a model, then the model’s GREML expectation can be
constructed with dataset.is.yX=TRUE in mxExpectationGREML().
casesToDrop
Numeric vector. Contains the indices of the rows of the ’y’ and ’X’ that were
dropped due to containing NA’s. Can be provided as as argument casesToDropFromV
to mxExpectationGREML().
References
The OpenMx User’s guide can be found at http://openmx.psyc.virginia.edu/documentation.
See Also
For more information generally concerning GREML analyses, including a complete example, see
mxExpectationGREML(). More information about the OpenMx package may be found here.
Examples
dat <- cbind(rnorm(100),rep(1,100))
colnames(dat) <- c("y","x")
dat[42,1] <- NA
dat[57,2] <- NA
dat2 <- mxGREMLDataHandler(data=dat, yvars="y", Xvars=list("x"),
addOnes = FALSE)
str(dat2)