\HeaderA{Multiple testing on the GO graph}{Multiple testing on the GO graph}{Multiple testing on the GO graph}
\aliasA{GAGO}{Multiple testing on the GO graph}{GAGO}
\aliasA{getFocus}{Multiple testing on the GO graph}{getFocus}
\aliasA{makeGOstructure}{Multiple testing on the GO graph}{makeGOstructure}
\keyword{htest}{Multiple testing on the GO graph}
\begin{Description}\relax
Three functions adapted from package \pkg{globaltest} to test (part of) the GO graph for
association of the gene expression profile of GO terms with a
response variable. Used together, these functions return
multiplicity-adjusted p-values calculated using the Focus Level
procedure that preserves the structure of the GO graph.
\end{Description}
\begin{Usage}
\begin{verbatim}
  GAGO(..., GO, focus, maxalpha = 0.05, stopafter = 100, verbose = FALSE)
  \end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{...}] Arguments describing the tests to be performed are passed on to \code{\LinkA{GlobalAncova}{GlobalAncova}}. 
Note that only the approximative version of \code{\LinkA{GlobalAncova}{GlobalAncova}} is used here and hence the parameter 
\code{method} is not available. Even though the number of permutations (\code{perm}) may be specified since
very large gene sets (with more genes than \code{max.group.size}) are treated with the permutation test.
\item[\code{GO}] An object of class \code{\LinkA{GOstructure}{GOstructure}} describing the structure of the GO
graph. This object should be created using \code{makeGOstructure}.
\item[\code{focus}] A vector of GO ids to describe te focus level. Typically made using \code{getFocus}.
\item[\code{maxalpha}] The maximum multiplicity-adjusted p-value. The algorithm will stop when this value is exceeded.
\item[\code{stopafter}] The maximum number of significant GO terms to be found. The algorithm will stop when this value is exceeded.
\item[\code{verbose}] If set to \code{TRUE}, prints much more extensive progress information.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Previous to a call to \code{GAGO}, first use \code{\LinkA{makeGOstructure}{makeGOstructure}} to make a GO graph tailored to a
specific data set. Then \code{\LinkA{getFocus}{getFocus}} can be used to choose a
focus level. Finally \code{GAGO} performs the focus level procedure.
\end{Details}
\begin{Value}
The function returns a named vector of multiplicity-adjusted
p-values. Adjusted p-values of GO terms not appearing in this vector
are larger than the chosen value of \code{maxalpha}.
\end{Value}
\begin{Note}\relax
Function \code{GAGO} corresponds to function \code{gtGO} in package \pkg{globaltest}. The
difference is in the use of the \code{GlobalAncova} test instead of \code{globaltest} within the focus level procedure.
\end{Note}
\begin{Author}\relax
Jelle Goeman: \email{j.j.goeman@lumc.nl}; Jan Oosting; Manuela Hummel
\end{Author}
\begin{References}\relax
Goeman, J.J. and Mansmann, U., Family-wise error rate on the directed acyclic 
graph of Gene Ontology, submitted.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{gtGO}{gtGO}}, \code{\LinkA{GlobalAncova}{GlobalAncova}}, \code{\LinkA{globaltest}{globaltest}}, 
\code{\LinkA{GOstructure}{GOstructure}}, \code{\LinkA{makeGOstructure}{makeGOstructure}}, \code{\LinkA{getFocus}{getFocus}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  # see vignettes of packages GlobalAncova and globaltest and help of gtGO
\end{ExampleCode}
\end{Examples}

