This command is used to get options which can be modified to control the behaviour of MultiPhen commands. It provides a list of options which are relevant to a particular command. For example, mPhen.assoc() has its behavioiur controlled by options in mPhen.options("regression"). In order to get a list of all options, you can type mPhen.options(descr=TRUE).
mPhen.options(type=c("regression", "plot", "geno.input",
"pheno.input","meta.analysis","misc"), descr = FALSE)A value which can take any of the following values: "regression", "plot","geno.input","pheno.input","meta.analysis","misc".
If set to TRUE, then returns descriptions of all the options. If FALSE, then returns the values of all the options.
A list of default option values. Note, the default value for opts = mPhen.options("regression"), has opts$inverseRegress =TRUE, opts$JointModel = TRUE and opts$geno.link = "ordinal", which is the standard multiPhen model.