alias.glmNA {Envisage} | R Documentation

## Find Aliases (Dependencies) in a Model

### Description

Find aliases (linearly dependent terms) in a linear model specified by a formula. This extends the S3 method `alias` to objects of class `glmNA` for package Envisage.

### Usage

      ## S3 method for class 'glmNA':
      alias(object, ...)

### Arguments

`object` | A fitted model object of class `glmNA`.
`...` | Further arguments passed to or from other methods.

### Details

The Envisage package contains methods allowing the use of linear models (LMs) for analysing significantly changing genes in experiments with a variety of sources of variation, be they experimentally controlled variables such as drug treatment or time, or non-controlled sources of confounding variation such as phenotypic or environmental differences. This allows all sources of variation to be considered when analysing for significant differential expression, ensuring resulting genes are biologically relevent to the experimental question.

The function `alias.glmNA` extends the method `alias` to the S4 class `glmNA` for package Envisage. This is an extension of classes `glm` and `lm` and deals appropriately with genes that produce NA calls in the modelling procedure. This allows use of the function `Anova` for calculating significance for each gene.

`alias.glmNA` is an internal function and is not designed to be accessed by users.

### Value

A list (of class "listof") containing components:

`Model` | Description of the model; usually the formula.
`Complete` | A matrix with columns corresponding to effects that are linearly dependent on the rows.
`Partial` | The correlations of the estimable effects, with a zero diagonal. An object of class "mtable" which has its own print method.

### Author(s)

Sam Robson S.C.Robson@warwick.ac.uk

### References

Robson, S. C., Hunter, E., Bird, H., Turner, H. (2008) Envisage: model-based significance analysis of microarray gene expression data, manuscript in preparation.

### See Also

`coef`, `glmNA. For the main \pkg{Envisage} method, see \code{envisage}.`

[Package Envisage version 1.0-2 Index]