macsR: Facilitate analysis of MACS results.

#' Facilitate analysis of MACS results
#' 
#' MACS (model based analysis for ChIP-Seq) is a popular program for converting
#' ChIP-Seq reads into peaks. If produces a number of output files in a
#' directory, which to my mind can be improved a little. This package imports
#' MACS results, improves the result files, and annotates peaks with their
#' nearest TSS and CpG island.
#' 
#' \code{\link{import.macs.peaks.file}} is used to import MACS results.
#' 
#' \code{\link{fix.macs.output}} is used to \sQuote{fix} or improve the
#' usability of MACS results, particularly for the end user who wants to get
#' genomic coordinates in UCSC-style strings, and get BED files of just the
#' significant peaks.
#' 
#' \code{\link{annotate.macs.output}} is used to annotate peaks by their
#' closest TSS or CpG island. This uses ChIPpeakAnno, and pre-built TSS and
#' CpG-island definitions, the former are from Ensembl, and the latter are from
#' UCSC.
#' 
#' @section macsR from the commandline:
#' I've included a few shell scripts inside the \code{bin} directory, which
#' can help run this code in offline mode. You can add this to your PATH,
#' eg on OSX: PATH=$PATH:/Library/Frameworks/R.framework/Resources/library/macsR/bin\cr
#' \code{do.macs.sh}: run MACS on 1 or 2 input bam files, fix the output & 
#' annotate the peaks with nearest TSS and CpG island. Note there are only a subset
#' of the macs14 options available.\cr
#' \code{fix.macs.sh}: fix/improve the look of MACS results.\cr
#' \code{annotate.macs.sh}: annotated MACS results with neares TSS and CpG
#'  islands. Note I always run this after running \code{fix.macs.sh}. I plan
#'  to allow you to add additional BED files for annotating peaks, though
#'  \code{bedtools} may be a better way to do this.
#' 
#' @section MACS version:
#' This package does not include macs, but it does expect macs14 to be installed &
#' on your path.
#' 
#' @section MACS installation on OSX 10.7.3:
#' Download the tar.gz: \url{https://github.com/downloads/taoliu/MACS/MACS-1.4.1.tar.gz}\cr
#' unpack & install to home dir:\cr
#' \code{$ python setup.py install --user}\cr
#' copy binaries from \code{./bin} to \code{~/bin/macs14} & make executable\cr
#' Edit \code{$HOME/.bashrc} file:\cr
#' \code{export PATH=$PATH:~/bin/macs14}\cr
#' \code{export PYTHONPATH=~/Library/Python/2.7/lib/python/site-packages:$PYTHONPATH}
#' 
#' @section MACS installation on Ubuntu:
#' Download & install the Debian package: \url{http://liulab.dfci.harvard.edu/MACS/Download.html}
#' 
#' @name macsR-package
#' @aliases macsR macsR-package
#' @docType package
#' @author Mark Cowley <m.cowley@@garvan.org.au>
#' @seealso \code{\link{import.macs.peaks.file}}, \code{\link{fix.macs.output}},
#'   \code{\link{annotate.macs.output}}
#' @references \url{http://liulab.dfci.harvard.edu/MACS/}
#' @keywords package
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