\name{sequenceCalc}
\alias{sequenceCalc}
\alias{sequenceCalc,GRanges,BSgenome-method}
\alias{sequenceCalc,data.frame,BSgenome-method}
\title{Find occurences of a DNA pattern}
\description{Function to find all occurrences of a DNA pattern in given locations.}
\usage{
  \S4method{sequenceCalc}{GRanges,BSgenome}(x, organism, pattern, fixed = TRUE, positions = FALSE)
  \S4method{sequenceCalc}{data.frame,BSgenome}(x, organism, window = NULL, positions = FALSE, ...)
}
\arguments{
  \item{x}{A \code{data.frame}, with columns \code{chr} and \code{position}, or instead of the column \code{position} there can be columns \code{start}, \code{end}, and \code{strand}, or a \code{GRanges} object of the regions.}
  \item{window}{Bases around the locations supplied in \code{x} that are in the window. Calculation will consider \code{windowSize/2-1} bases upstream, and \code{windowSize/2} bases downstream.}
  \item{organism}{The \code{BSgenome} object to calculate CpG density upon.}
  \item{pattern}{The \code{DNAString} to search for.}
  \item{fixed}{Whether to allow degenerate matches.}
  \item{positions}{If \code{TRUE}  \code{FALSE}}
  \item{...}{Arguments passed into the \code{GRanges} method}
}
\details{If the version of the data frame with the start, end, and strand columns is given, the window will be created around the TSS.}
\value{
  If \code{positions} is \code{TRUE}, a list of vectors of positions of matches in relation to the elements of \code{x}, otherwise a \code{vector} of the number of matches for each element of \code{x}.
}
\seealso{\code{\link{cpgDensityCalc}}, \code{\link{mappabilityCalc}}, \code{\link{gcContentCalc}}}
\author{Aaron Statham}
\examples{
require(BSgenome.Hsapiens.UCSC.hg18)
TSSTable <- data.frame(chr=paste("chr",c(1,2),sep=""), position=c(100000,200000))
sequenceCalc(TSSTable, 600, organism=Hsapiens, pattern=DNAString("CG"))
}