\HeaderA{rawCd4DnaseI}{A data frame with information on the UCSC
browser track related to DNaseI hypersensitivity}{rawCd4DnaseI}
\aliasA{rawCD4}{rawCd4DnaseI}{rawCD4}
\aliasA{rawHelaDnaseI}{rawCd4DnaseI}{rawHelaDnaseI}
\keyword{models}{rawCd4DnaseI}
\begin{Description}\relax
A data frame with information on the UCSC
browser track related to DNaseI hypersensitivity; the
rawCD4 object is an eSet extension representing the
same information; rawHelaDnaseI is like rawCD4 but results
on Hela cells.
\end{Description}
\begin{Usage}
\begin{verbatim}
data(rawCd4DnaseI)
data(rawHelaDnaseI)
data(rawCD4)
\end{verbatim}
\end{Usage}
\begin{Details}\relax
Obtained from a MySQL representation of the data 
distributed at the Genome Browser FTP site
\end{Details}
\begin{Value}
a data.frame
\end{Value}
\begin{Author}\relax
Vince Carey <stvjc@channing.harvard.edu>
\end{Author}
\begin{References}\relax
\url{hgdownload.cse.ucsc.edu} ... it appears
that they do not offer the MYD/MYI representations, just
the txt.gz and sql files now.   So if you obtain
the encodeNhgriDnaseHsChipRawCd4.txt and .sql files
at goldenPath/currentGenomes/Homo\_Sapiens/encode/database,
you can reconstruct the underlying data for this data.frame
(hg18, Nov 2007).
\end{References}
\begin{Examples}
\begin{ExampleCode}
data(rawCd4DnaseI)
dim(rawCd4DnaseI)
rawCd4DnaseI[1:5,]
library(lattice)
xyplot(dataValue~chromStart|chrom, data=rawCd4DnaseI, subset=chrom %in%
  c("chr1", "chr10", "chr19", "chr20"), scales=list(x=list(relation="free"))) 
\end{ExampleCode}
\end{Examples}

