\Header{makeContrasts}{Construct Matrix of Custom Contrasts}
\keyword{regression}{makeContrasts}
\begin{Description}\relax
Construct the contrasts matrix corresponding to specified contrasts of a set of given parameters.
\end{Description}
\begin{Usage}
\begin{verbatim}
makeContrasts(..., levels) 
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{...}] expressions, or character strings which can be parsed to expressions, specifying contrasts
\item[\code{levels}] character vector giving the names of the parameters to be contrasts, or a factor or design matrix from which the names can be extracted.
\end{ldescription}
\end{Arguments}
\begin{Value}
Matrix which columns corresponding to contrasts.\end{Value}
\begin{Author}\relax
Gordon Smyth
\end{Author}
\begin{SeeAlso}\relax
An overview of linear model functions in limma is given by \link{5.LinearModels}.
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
makeContrasts(B-A,C-B,C-A,levels=c("A","B","C"))
makeContrasts("A","B","B-A",levels=c("A","B"))
\end{ExampleCode}
\end{Examples}

