\HeaderA{nem.jackknife}{Jackknife for nested effect models}{nem.jackknife}
\aliasA{print.nem.jackknife}{nem.jackknife}{print.nem.jackknife}
\keyword{models}{nem.jackknife}
\begin{Description}\relax
Assesses the statistical stability of a network via a jackknife procedure: Each S-gene is left out once and the network reconstructed on the remaining ones. The relative frequency of each edge to appear in n-1 jackknife samples is returned.
\end{Description}
\begin{Usage}
\begin{verbatim}
nem.jackknife(D, thresh=0.5, inference="nem.greedy",models=NULL,control=set.default.parameters(unique(colnames(D))), verbose=TRUE)

## S3 method for class 'nem.jackknife':
print(x, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{D}] data matrix with experiments in the columns (binary or continious)
\item[\code{thresh}] only edges appearing with a higher frequency than "thresh" are returned
\item[\code{inference}] \code{search} to use exhaustive enumeration, \code{triples} for triple-based inference, \code{pairwise} for the pairwise heuristic, \code{ModuleNetwork} for the module based inference, \code{nem.greedy} for greedy hillclimbing, \code{nem.greedyMAP} for alternating MAP optimization using log odds or log p-value densities
\item[\code{models}] a list of adjacency matrices for model search. If NULL, an  exhaustive enumeration of all possible models is performed.
\item[\code{control}] list of parameters: see \code{set.default.parameters}
\item[\code{verbose}] do you want to see progression statements? Default: TRUE
\item[\code{x}] nem object
\item[\code{...}] other arguments to pass
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Calls \code{\LinkA{nem}{nem}} or \code{\LinkA{nemModelSelection}{nemModelSelection}} internally, depending on whether or not parameter lambda is a vector and parameter Pm != NULL.
\end{Details}
\begin{Value}
nem object with edge weights being the jackknife probabilities
\end{Value}
\begin{Author}\relax
Holger Froehlich
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{nem.bootstrap}{nem.bootstrap}}, \code{\LinkA{nem.consensus}{nem.consensus}}, \code{\LinkA{nem}{nem}}, \code{\LinkA{nemModelSelection}{nemModelSelection}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## Not run: 
   data("BoutrosRNAi2002")
   D <- BoutrosRNAiDiscrete[,9:16]
   nem.jackknife(D, control=set.default.parameters(unique(colnames(D)), para=c(0.13,0.05)))         
## End(Not run)
\end{ExampleCode}
\end{Examples}

