\HeaderA{coef.glmNA}{Extract Model Coefficients}{coef.glmNA}
\keyword{models}{coef.glmNA}
\begin{Description}\relax
\code{\LinkA{coef}{coef}} is a generic function which extracts model
coefficients from objects returned by modeling
functions. \code{coefficients} is an \emph{alias} for it. This extends
the S3 method  \code{\LinkA{coef}{coef}} to objects of class
\code{\LinkA{glmNA}{glmNA}} for package \pkg{Envisage}.
\end{Description}
\begin{Usage}
\begin{verbatim}
  ## S3 method for class 'glmNA':
  coef(object, ...) 
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] A fitted model object of class
\code{\LinkA{glmNA}{glmNA}}.
\item[\code{...}] Further arguments passed to or from other methods.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The \pkg{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 \code{\LinkA{coef.glmNA}{coef.glmNA}} extends the method
\code{\LinkA{coef}{coef}} to the S4 class
\code{\LinkA{glmNA}{glmNA}} for package
\pkg{Envisage}. This is an extension of classes \code{glm} and
\code{lm} and deals appropriately with the model output for genes that
produce NA calls in the modelling procedure. This allows use of the
function \code{\LinkA{Anova}{Anova}} for calculating significance for
each gene. 

\code{\LinkA{alias.glmNA}{alias.glmNA}} is an internal function and is not
designed to be accessed by users.
\end{Details}
\begin{Value}
Coefficients extracted from the model object \code{object}.
\end{Value}
\begin{Author}\relax
Sam Robson \email{S.C.Robson@warwick.ac.uk}
\end{Author}
\begin{References}\relax
Robson, S. C., Hunter, E., Bird, H., Turner, H. (2008) 
\emph{Envisage: model-based significance analysis of microarray gene expression data}, 
manuscript in preparation.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{alias}{alias}},
\code{\LinkA{glmNA}{glmNA}}. For the main \pkg{Envisage} method, see
\code{\LinkA{envisage}{envisage}}.
\end{SeeAlso}

