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]