\name{extractSpectra-methods}
\docType{methods}
\alias{extractSpectra-methods}
\alias{extractSpectra}


\title{ Extracts a set of spectra from an 'MSnExp' object }

\description{
  Extracts the spectra defined by the \code{selected} parameter and
  returns a subset \code{"\linkS4class{MSnExp}"} instance. The
  \code{featureData} slot is also subset accordingly.

  Note that values in \code{selected} are recycled if shorter than
  \code{length(MSnExp)}.

  This method is equivalent as using the \code{[} operator.
}

\section{Methods}{
  \describe{
    \item{\code{signature(object = "MSnExp", selected = "logical")}}{
      Returns an \code{"\linkS4class{MSnExp}"} object containing spectra 
      defined by the logical \code{selected} argument.
    }
  }
}

\author{
  Laurent Gatto <lg390@cam.ac.uk>
}

\seealso{
  \code{\link{extractPrecSpectra}}
}

\examples{
fn <- dir(system.file(package = "MSnbase", dir = "extdata"),
          full.names = TRUE,
          pattern = "mzXML$")
aa <- readMSData(fn, verbose=FALSE)
sel <- rep(FALSE, length(aa))
sel[1:3] <- TRUE
bb <- extractSpectra(aa, sel)
stopifnot(length(bb) == sum(sel))
processingData(bb)
## equivalent
cc <- aa[sel]
all(featureNames(cc) == featureNames(bb))
}

\keyword{methods}