\name{writeWig}
\alias{writeWig}
\alias{writeWig,AffymetrixCelSet-method}
\alias{writeWig,GRangesList-method}
\title{Writes sequencing data out into wiggle files}
\description{Writes sequencing data out into wiggle files}
\usage{
  \S4method{writeWig}{AffymetrixCelSet}(rs, design=NULL, log2.adj=TRUE, verbose=TRUE)
  \S4method{writeWig}{GRangesList}(rs, seq.len = NULL, design=NULL, sample=20, drop.zero=TRUE, normalize=TRUE, verbose=TRUE)
}
\arguments{
  \item{rs}{The sequencing or array data.}
  \item{design}{design matrix specifying the contrast to compute (i.e. the samples to use and what differences to take)}
  \item{log2.adj}{whether to take log2 of array intensities.}
  \item{verbose}{Whether to write progress to screen}
  \item{seq.len}{If sequencing reads need to be extended, the fragment size to be used}
  \item{sample}{At what basepair resolution to sample the genome at}
  \item{drop.zero}{Whether to write zero values to the wiggle file - TRUE saves diskspace}
  \item{normalize}{Whether to normalize each lane to its total number of reads, TRUE is suggested}
}
\details{
A wiggle file is created for each column in the design matrix (if design is left as NULL, then a file 
is created for each array/lane of sequencing). The filenames are given by the column names of the design
matrix, and if ending in "gz" will be written out as a gzfile. 
}
\value{Wiggle file(s) are created}
\author{
Aaron Statham
}
\examples{
#See examples in the manual
}