\HeaderA{adjPval}{Generate FDR adjusted P values for F test result.}{adjPval}
\keyword{utilities}{adjPval}
\begin{Description}\relax
This function takes a result object from \code{\LinkA{matest}{matest}}
and calculate the FDR adjusted P values. The new P values will be
appended to the input object as additional fields. It has four
options;  "stepup" (Hochberg and Benjamini, 1990), "adaptive" (Benjamini and Hochberg, 2000), "stepdown" (Westfall and Young, 1993) and "jsFDR" (Storey,
2002). "jsFDR" option uses 'qvalue' package by John Storey and user suppose
to install 'qvalue' package before using this option. There is no default
option, thus you need to specify one option.
\end{Description}
\begin{Usage}
\begin{verbatim}
adjPval(matestobj, method=c("stepup","adaptive", "stepdown", "jsFDR"))
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{matestobj}] An object of class \code{matest}, which is the result
from \code{\LinkA{matest}{matest}}.
\item[\code{method}] The method for FDR control.
\end{ldescription}
\end{Arguments}
\begin{Value}
An object of class \code{matest} with the following fields added for
each F test:
\begin{ldescription}
\item[\code{adjPtab}] FDR adjusted tabulated P values.
\item[\code{adjPvalperm}] FDR adjusted permutation P values.
\end{ldescription}
\end{Value}
\begin{Author}\relax
Hao Wu
\end{Author}
\begin{Examples}
\begin{ExampleCode}
data(abf1)
## Not run: 
 
fit.full.simple = fitmaanova(abf1,formula = ~Strain)
# F-test strain effect
ftest.all = matest(abf1, fit.full.simple, term="Strain",n.perm= 1000)
# make FDR adjusted P values
ftest.all = adjPval(ftest.all, 'jsFDR')
# there will be new fields in test.strain.fix after this
## End(Not run)
\end{ExampleCode}
\end{Examples}

