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\name{findLargeGaps}
\alias{findLargeGaps.default}
\alias{findLargeGaps}
\alias{findLargeGaps.data.frame}

\title{Identifies gaps of a genome where there exist no observations}

\description{
 Identifies gaps of a genome where there exist no observations.
}

\usage{
\method{findLargeGaps}{default}(chromosome=NULL, x, minLength, resolution=1L, ...)
}

\arguments{
  \item{chromosome}{(Optional) An \code{\link[base]{integer}} \code{\link[base]{vector}} of length J of
    chromosome indices.}
  \item{x}{A \code{\link[base]{numeric}} \code{\link[base]{vector}} of J of genomic locations.}
  \item{minLength}{A positive \code{\link[base]{numeric}} scalar specifying the minimum
    length of a gap.}
  \item{resolution}{A non-negative \code{\link[base]{numeric}} specifying the minimum
    length unit, which by default equals one nucleotide/base pair.}
  \item{...}{Not used.}
}

\value{
  Returns \code{\link[base]{data.frame}} zero or more rows and with columns
  \code{chromosome} (if given), \code{start}, \code{stop},
  and \code{length}.
}

\author{Henrik Bengtsson}

\seealso{
  Use \code{\link{gapsToSegments}}() to turn the set of identified gaps into
  the complementary set of segments such that they can be passed
  to \code{\link{segmentByCBS}}(), \code{\link{segmentByPairedPSCBS}}() and
  \code{\link{segmentByNonPairedPSCBS}}() via argument \code{knownSegments}.
}


\keyword{IO}
