\name{relocateObject}
\alias{relocateObject}
\alias{relocateObject,CNSet-class}
\title{Changes filename and pattern attributes for ff objects. }
\description{
	See details
}
\usage{
relocateObject(object, to)
}

\arguments{
  \item{object}{
	  An object of class \code{CNSet}.
  }
  \item{to}{
    Character string indicating complete path to ff objects.
  }
}
\details{

This function is experimental

When crlmm is used in conjunction with the ff package, large files are
saved as ff_matrix of ffdf objects to avoid excessive RAM.  The R object
in RAM contains pointers to the location on disk.  If the files on disk
are moved, the data can no longer be accessed through the R object in
memory.  However, if the pointers contained in the R object are modified
to point to the new location, the data can be accessed as usual.  The
\code{relocateObject} function edits the pointers of all ff objects
embedded within the \code{CNSet} class. In particular, all elements
stored in slot \code{assayData} and all elements stored in slot
\code{batchStatistics}.

}
\value{
	An object of class \code{CNSet}.
}

\author{
R. Scharpf and L. Mireless
}
\seealso{
	\code{\link{CNSet-class}}
}
\examples{
	\dontrun{
		require(ff)
		cdfName <- "genomewidesnp6"
		pathToCels <- "/thumper/ctsa/snpmicroarray/hapmap/raw/affy/1m"
		outdir <- file.path(getwd(), "ff")
		if(!file.exists(outdir)) stop("Please specify a valid directory for storing output")
		if(!file.exists(pathToCels)) stop("Please specify the correct path to the CEL files")
		celFiles <- list.celfiles(pathToCels, full.names=TRUE, pattern=".CEL")[1:6]
		batch <- as.factor(substr(basename(celFiles), 13, 13))
		ldPath(outdir)
		ocProbesets(100e3)
		ocSamples(200)
		gtSet(celFiles, cdfName, batch=batch)
		A(gtSet)[1:5, ]
		pattern(A(gtSet))
		filename(A(gtSet))
                ## Move all ff files to directory called 'testing'
		outdir2 <- file.path(getwd(), "testing")
		relocateObject(gtSet, to=outdir2)
		## note the pointers have changed
		pattern(A(gtSet))
		filename(A(gtSet))
	}
}
\keyword{manip}