A data frame with information on the UCSC browser track related to DNaseI hypersensitivity

Description

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.

Usage

data(rawCd4DnaseI)
data(rawHelaDnaseI)
data(rawCD4)

Details

Obtained from a MySQL representation of the data distributed at the Genome Browser FTP site

Value

a data.frame

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

References

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).

Examples

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")))