mPhen.options: Retrieves default mPhen options, and descriptions.

Description Usage Arguments Value

Description

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).

Usage

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mPhen.options(type=c("regression", "plot", "geno.input",
"pheno.input","meta.analysis","misc"), descr = FALSE)

Arguments

type

A value which can take any of the following values: "regression", "plot","geno.input","pheno.input","meta.analysis","misc".

descr

If set to TRUE, then returns descriptions of all the options. If FALSE, then returns the values of all the options.

Value

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.



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