rawCd4DnaseI {encoDnaseI} | R Documentation

## 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")))

[Package encoDnaseI version 0.1-0 Index]