\name{shrinkageFun-method}
\alias{shrinkageFun}
\usage{
## For IRanges
\S4method{shrinkageFun}{IRanges}(obj, max.gap = 1L)

## For GenomicRanges
\S4method{shrinkageFun}{GenomicRanges}(obj, max.gap = 1L)
}
\title{Shrinkage function}
\description{Create a shrinkage function based on specified gaps and shrinkage rate.}
\details{\code{shrinkageFun} function will read in a GenomicRanges object
which represent the gaps, and return a function which works for
another GenomicRanges object, to shrink that object based on
previously specified gaps shrinking information.  You could use
this function to treat multiple tracks(e.g. GRanges) to make sure
they shrunk based on the common gaps and the same ratio.}
\value{A shrinkage function which could shrink a GenomicRanges
object}
\docType{methods}
\alias{shrinkageFun,GenomicRanges-method}
\alias{shrinkageFun,IRanges-method}
\author{Tengfei Yin}
\arguments{\item{obj}{GenomicRanges object which represent gaps}
\item{max.gap}{Gaps to be kept, it's a fixed value, if this value
is bigger than certain gap interval, then that gap is not going to
be shrunk.}
}
\examples{
library(GenomicRanges)
gr1 <- GRanges("chr1", IRanges(start = c(100, 300, 600),
                               end = c(200, 400, 800)))
shrink.fun1 <- shrinkageFun(gaps(gr1), max.gap = maxGap(gaps(gr1), 0.15))
shrink.fun2 <- shrinkageFun(gaps(gr1), max.gap = 0)
shrink.fun1(gr1)
shrink.fun2(gr1)
}