\name{stab.fs}
\alias{stab.fs}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{
Function to quantify stability of feature selection.
}
\description{
This function computes several indexes to quantify feature selection stability. This is usually estimated through perturbation of the original dataset by generating multiple sets of selected features.
}
\usage{
stab.fs(fsets, N, method = c("kuncheva", "davis"), ...)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{fsets}{ list of sets of selected features, each set of selected features may have different size }
  \item{N}{ total number of features on which feature selection is performed }
  \item{method}{ stability index (see details section) }
  \item{\dots}{ additional parameters passed to stability index (\code{penalty} that is a numeric for Davis' stability index, see details section) }
}
\details{
Stability indices may use different parameters. In this version only the Davis index requires an additional parameter that is \code{penalty}, a numeric value used as penalty term.

Kuncheva index (\code{kuncheva}) lays in [-1, 1], An index of -1 means no intersection between sets of selected features, +1 means that all the same features are always selected and 0 is the expected stability of a random feature selection.

Davis index (\code{davis}) lays in [0,1], With a pnalty term equal to 0, an index of 0 means no intersection between sets of selected features and +1 means that all the same features are always selected. A penalty of 1 is usually used so that a feature selection performed with no or all features has a Davis stability index equals to 0. None estimate of the expected Davis stability index of a random feature selection was published.
}
\value{ A numeric that is the stability index }
\references{
Davis CA, Gerick F, Hintermair V, Friedel CC, Fundel K, Kuffner R, Zimmer R (2006) "Reliable gene signatures for microarray classification: assessment of stability and performance", \emph{Bioinformatics}, \bold{22}(19):356-2363.

Kuncheva LI (2007) "A stability index for feature selection", \emph{AIAP'07: Proceedings of the 25th conference on Proceedings of the 25th IASTED International Multi-Conference}, pages 390--395.
}
\author{
Benjamin Haibe-Kains
}
%%\note{}

%% ~Make other sections like Warning with \section{Warning }{....} ~

\seealso{
\code{\link[genefu]{stab.fs.ranking}}
}
\examples{
set.seed(54321)
## 100 random selection of 50 features from a set of 10,000 features
fsets <- lapply(as.list(1:100), function(x, size=50, N=10000) {
  return(sample(1:N, size, replace=FALSE))} )
names(fsets) <- paste("fsel", 1:length(fsets), sep=".")

## Kuncheva index
stab.fs(fsets=fsets, N=10000, method="kuncheva")
## close to 0 as expected for a random feature selection

## Davis index
stab.fs(fsets=fsets, N=10000, method="davis", penalty=1)

}
\keyword{ feature selection }
\keyword{ stability }