\HeaderA{fga.func}{Function to compute fraction of genome altered for each sample}{fga.func}
\keyword{htest}{fga.func}
\begin{Description}\relax
This function outputs lists containing proportions of the genome that
are gained and lost for each sample.
\end{Description}
\begin{Usage}
\begin{verbatim}
fga.func(aCGH.obj, thres = 0.25, factor = 2.5, 
         samplenames = sample.names(aCGH.obj), 
         chrominfo = human.chrom.info.Jul03)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{aCGH.obj}] An object of aCGH class
\item[\code{thres}] either a vector providing unique threshold for
each sample or a vector of the same length as number of
samples providing sample-specific
threshold. If 'aCGH.obj' has non-null 'sd.samples', then
threshold is automatically replaced by tumor-specific sd
multiplied by 'factor'. Clone is considered to be gained if
it is above the threshold and lost if it is below negative
threshold. Defaults to 0.25
\item[\code{factor}] specifies the number by which experimental
variability should be multiples. Used only when tumor
specific variability in 'aCGH.obj' is not NULL or when factor is greater than 0. Defaults to
2.5.
\item[\code{samplenames}] Sample names. Default is sample.names(aCGH.obj)
\item[\code{chrominfo}] A chromosomal information associated with the mapping of the
data. Default is human.chrom.info.Jul03 data frame
\end{ldescription}
\end{Arguments}
\begin{Value}
\begin{ldescription}
\item[\code{gainP}] Vector of proportion of genome gained for each sample
\item[\code{lossP}] Vector of proportion of genome lost for each sample
\end{ldescription}
\end{Value}
\begin{Author}\relax
Jane Fridlyand, Ritu Roydasgupta
\end{Author}
\begin{Examples}
\begin{ExampleCode}

data(colorectal)

col.fga <- fga.func(colorectal, factor=3,chrominfo=human.chrom.info.Jul03)
cbind(gainP=col.fga$gainP,lossP=col.fga$lossP)[1:5,]

\end{ExampleCode}
\end{Examples}

