Usage
solarPolygenic(formula, data, dir, kinship, traits, covlist = "1",
covtest = FALSE, screen = FALSE, household = as.logical(NA),
transforms = character(0), alpha = 0.05, polygenic.settings = "",
polygenic.options = "", verbose = 0, ...)
Arguments
formula
an object of class formula or one that can be coerced to that class.
It is a symbolic description of fixed effects (covariates) to be fitted.
If the model does not have any covariates, then the formula looks like
trait ~ 1, where
data
A data frame containing the variables in the model,
including ID fields needed to construct random effects: genetic and house-hold (both optional).
Other classes such as list, environment or object coercible by as.data.frame to a data frame
a
dir
an optional character string, the name of directory,
where SOLAR performs the analysis.
In this case, the analysis within related input/output files is
conducted in the given folder instead of a temporary one
(the default work flow).
kinship
A matrix of the kinship coefficients (custom kinship matrix).
The IDs are required to be in row and column names.
Currently, it does not work for unrelated individuals (SOLAR issue).
traits
a vector of characters to specify trait(s) in the model. It is alternative to the formula interface.
covlist
a vector of characters to specify fixed effects (covariates) in the model.
It is alternative to the formula interface.
It could be convenient to indicate covariates in the SOLAR format,
for example, "age^1,2,3#sex" that means sex age ag
covtest
a logical value, indicating whether to test the significance of the fixed effects (covariates).
Likelihood ratio test (LRT) is used by SOLAR.
polygenic SOLAR command is called with a combination of -screen -all options.
As a resu
screen
a logical value, indicating whether to screen the fixed effects (covariates).
polygenic SOLAR command is called with -screen option.
As a result, only significant covariates will be maintained in the model.
The default value is <
household
a logical value, saying to forcedly include or exclude the house-hold effect.
The default value is as.logical(NA), that means the following behavior in SOLAR.
If data has hhid or similar column,
then
transforms
a named vector of characters, indicating the transformations to be applied to traits.
A list of available transforms is returned by function availableTransforms.
If the model is univariate, the alpha
a number between 0 an 1, that is the value of
-prob option of polygenic SOLAR command.
That is the probability level for keeping covariates as significant.
The default value in SOLAR is 0.1,
but the default value here is 0.
polygenic.settings
A vector of characters, that contains SOLAR commands to be executed just before calling polygenic.
For example, the liability threshold model applied to a binary trait (the default behavior in SOLAR).
This behavior is disabled by setting the
polygenic.options
A character of options to be passed to polygenic SOLAR command.
For example, the comprehensive analysis of a bivariate model might be parametrized
by setting this parameter to "-testrhoe -testrhog -testrhoc -testrhop -rhopse".
Se
verbose
An non-negative integer of the verbose level.
The default value is 0.
...
additional parameters to be passed to other functions called inside of solarPolygenic.
For example, it might be a parameter log.base for transformTrait function
in the