\name{getAllPeakSequence}
\alias{getAllPeakSequence}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{ Obtain genomic sequences around the peaks
 }
\description{
  Obtain genomic sequences around the peaks leveraging BSgenome and biomaRt package
}
\usage{
getAllPeakSequence(myPeakList, upstream = 200, downstream = 200, genome, AnnotationData)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{myPeakList}{ RangedData: See example below}
  \item{upstream}{upstream offset from the peak start, e.g., 200 }
  \item{downstream}{ downstream offset from the peak end, e.g., 200 }
  \item{genome}{ BSgenome object or mart object. Please refer to available.genomes in BSgenome package and useMart in bioMaRt package for details}
   \item{AnnotationData}{ RangedData used if mart object is parsed in which can be obtained from getAnnotation with featureType="TSS". For example, data(TSS.human.NCBI36), data(TSS.mouse.NCBIM37), data(GO.rat.RGSC3.4) and data(TSS.zebrafish.Zv8).  If not supplied, then annotation will be obtained from biomaRt automatically using the mart object}
}
\details{
 
}
\value{
 RangedData with slot start holding the start position of the peak, slot end holding the end position of the peak, slot rownames holding the id of the peak and slot space holding the chromosome location where the peak is located. In addition, the following variables are included.
 \item{upstream}{upstream offset from the peak start}
 \item{downstream}{downstream offset from the peak end}
\item{sequence}{the sequence obtained}
}
\references{ Durinck S. et al. (2005) BioMart and Bioconductor: a powerful link between biological biomarts and microarray data analysis. Bioinformatics, 21, 3439-3440. }
\author{ Lihua Julie Zhu }
\note{ 


}
\seealso{  }
\examples{
	#### use Annotation data from BSgenome
	peaks = RangedData(IRanges(start=c(100, 500), end=c(300, 600), names=c("peak1", "peak2")), space=c("NC_008253", "NC_010468"))
	library(BSgenome.Ecoli.NCBI.20080805)
 	seq = getAllPeakSequence(peaks, upstream = 20,
	downstream = 20, genome = Ecoli)
	write2FASTA(seq)
}

% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
\keyword{ misc }