\HeaderA{aCGH.test}{Testing association of aCGH clones with censored or continuous
outcomes}{aCGH.test}
\aliasA{mt.maxT}{aCGH.test}{mt.maxT}
\aliasA{mt.minP}{aCGH.test}{mt.minP}
\keyword{htest}{aCGH.test}
\begin{Description}\relax
\code{aCGH.test} function tests for association of each clone in an
univariate manner with censored or continous outcome by fitting Cox
proportional hazards model or linear regression model. There is also
an alternative to Cox prop. hazards - testing for differences in
survival curves defined by the groups in the outcome variable using
the \eqn{G^\rho}{} family of tests.
\end{Description}
\begin{Usage}
\begin{verbatim}
aCGH.test(aCGH.obj, rsp, test = c("survdiff","coxph",
          "linear.regression"), p.adjust.method = "fdr",imputed=TRUE, 
           subset = NULL, strt = NULL, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{aCGH.obj}] aCGH object containing clones' log2 ratios. 
\item[\code{rsp}] Response variable which is either \code{\LinkA{Surv}{Surv}}
object from \code{survival} package or continous outcome.
\item[\code{test}] Currently only three values are allowed - "coxph",
"survdiff", and "linear.regression", which test for association
using Cox proportional hazards model, \eqn{G^\rho}{} family of tests
(\code{\LinkA{survdiff}{survdiff}}) or linear model.

\item[\code{p.adjust.method}] This is a parameter controlling how the
p-values from the univariate tests are going to be adjusted for
multiple testing. Default value is Benjamini \& Hochberg (1995) FDR
method. Please refer to \code{\LinkA{p.adjust}{p.adjust}} function for more
help.
\item[\code{imputed}] Whether imputed or original log2ratios should be
used. Default is TRUE (imputed).
\item[\code{subset}] Specifies subset index of clones to be tested.
\item[\code{strt}] Aptional strata variable for splitting the data in
different strata.
\item[\code{...}] Optional parameters passed further along to each of the
univariate testing functions.
\end{ldescription}
\end{Arguments}
\begin{Value}
A data frame similar to the result returned from
\code{\LinkA{mt.maxT}{mt.maxT}} function from \code{multtest} package with
components:
\begin{ldescription}
\item[\code{index}] Vector of row indices, between 1 and \code{nrow(X)}, where rows are
sorted first according to their adjusted \eqn{p}{}-values, next their
unadjusted \eqn{p}{}-values, and finally their test statistics.

\item[\code{teststat}] Vector of test statistics, ordered according to \code{index}. To get
the test statistics in the original data order, use
\code{teststat[order(index)]}.

\item[\code{rawp}] Vector of raw (unadjusted) \eqn{p}{}-values, ordered according to
\code{index}.

\item[\code{adjp}] Vector of adjusted \eqn{p}{}-values, ordered according to
\code{index}.

\end{ldescription}
\end{Value}
\begin{Author}\relax
Peter Dimitrov
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{aCGH}{aCGH}}, \code{\LinkA{Surv}{Surv}}, \code{\LinkA{mt.maxT}{mt.maxT}},
\code{\LinkA{coxph}{coxph}}, \code{\LinkA{survdiff}{survdiff}}, \code{\LinkA{p.adjust}{p.adjust}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
\end{ExampleCode}
\end{Examples}

