plrs.test {plrs} | R Documentation

## Likelihood ratio test for a `plrs` model

### Description

Test whether copy number has an effect on mRNA expression.

### Usage

    plrs.test(object, alpha=0.05)

### Arguments

`object` | An object of class `plrs-class`
`alpha` | Significance level

### Details

Two cases present themselves:
1. The model is unconstrained. Thus, the model under the null hypothesis is the intercept and an F-test is performed.
2. The model is constrained and the following hypothesis are tested:
H0: All constraints are actives (=)
H1: At least one constraint is strict (>)
Under H0, we always have the intercept model. Indeed, if `constr.slopes = 1` (or 2) and `constr.intercepts = T`, then the only parameter free of inequality constraint is the overall intercept. If `constr.intercepts = F`, the local intercepts are additionnaly constrained to be 0 in order to obtain the intercept model under the null. The likelihood ratio statistic (unknown variance) is asymptotically distributed as a weighted mixture of Beta distribution (cf Gromping (2010)). Calculation of p-values is based on functions `ic.weights` and `pbetabar` of package ic.infer. The package mvtnorm is also involved.
In both cases the input model is taken as the model under the alternative.

### Value

A `list` object with the following components:

`stat` | Test statistic
`pvalue` | Calculated pvalue
`wt.bar` | Weights (if the model is constrained)
`df.bar` | Degrees of freedom.
`unconstr` | Unconstrained model of class `plrs-class`
`qbetabar` | (1-`alpha`) quantile of the beta mixture distribution
`alpha` | Significance level

### Author(s)

Gwenael G.R. Leday g.g.r.leday@vu.nl

### References

Gromping, U. (2010). Inference with linear equality and inequality constraints using R: The package ic.infer. J Stat Softw, 33(i10).

### Examples

    # Simulate data
    sim <- plrs.sim(n=80, states=2, sigma=0.5)

    # Fit a model
    model <- plrs(expr=sim$expr, cghseg=sim$seg, cghcall=sim$cal)

    # Testing
    model <- plrs.test(model)
    model

[Package plrs version 1.26.0 Index]