\HeaderA{getFDgene}{Get fitness defect genes}{getFDgene}
\keyword{data}{getFDgene}
\keyword{manip}{getFDgene}
\begin{Description}\relax
Function to select genes that present a significant growth defect
according to the condition(media) or generation time.
\end{Description}
\begin{Usage}
\begin{verbatim}
getFDgene(data,condition,cutoff,mode="generation",subset)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{data}] List of fitness defect scores for genes tested at
different experimental conditions.
\item[\code{condition}] Dataframe of experimental conditions
\item[\code{cutoff}] Numerical vector of length one or more, defining the threshold of
'significance' for the fitness defect score
\item[\code{mode}] Character string defining the base of the selection either
'condition' (media) or 'generation' time, Default=generation.
\item[\code{subset}] Numerical vector or list to which apply the different cutoffs.
\end{ldescription}
\end{Arguments}
\begin{Value}
Reduced list of gene fitness scores per experimental condition
according to the experimental condition or the generation time.
\end{Value}
\begin{Author}\relax
N. LeMeur
\end{Author}
\begin{References}\relax
Giaever G. et al. (2002) Functional profiling of the Saccharomyces cerevisiae
genome. Nature. 418(6896):387-91. PMID: 12140549
\end{References}
\begin{Examples}
\begin{ExampleCode}
 data(GiaeverPheno)
 data(GiaeverExpCdt)
 ##Select all the genes, in the different experimental conditions, that present a fitness score above 20, 100 and 100 at 5, 15 and 20 generations, respectively 
 fitnessGen <- getFDgene(GiaeverPheno,condition=GiaeverExpCdt,cutoff=c(20,100,100),mode="generation",subset=c(5,15,20))
 ##Select all the genes, that present a fitness score above 15 and 100
 ##in the condition set A and B respectively, independently of the generation time 
fitnessCondt <- getFDgene(GiaeverPheno,condition=GiaeverExpCdt,cutoff=c(100,15),mode="condition",subset=list(a=c(1:23,27,30,31),b=c(24:26,28,29)))
\end{ExampleCode}
\end{Examples}

