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"))) 

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(encoDnaseI)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: lattice
Loading required package: GGtools
Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Loading required package: data.table
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    colMeans, colSums, expand, rowMeans, rowSums

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums


Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene

Attaching package: 'GGtools'

The following object is masked from 'package:stats':

    getCall

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/encoDnaseI/encoDnaseI.Rd_%03d_medium.png", width=480, height=480)
> ### Name: rawCd4DnaseI
> ### Title: A data frame with information on the UCSC browser track related
> ###   to DNaseI hypersensitivity
> ### Aliases: rawCd4DnaseI rawHelaDnaseI rawCD4
> ### Keywords: models
> 
> ### ** Examples
> 
> data(rawCd4DnaseI)
> dim(rawCd4DnaseI)
[1] 382713      5
> rawCd4DnaseI[1:5,]
   bin chrom chromStart  chromEnd dataValue
1 1725  chr1  149424685 149424734     0.336
2 1725  chr1  149424723 149424772     0.292
3 1725  chr1  149424761 149424810     0.344
4 1725  chr1  149424799 149424848     0.542
5 1725  chr1  149424837 149424886     0.166
> library(lattice)
> xyplot(dataValue~chromStart|chrom, data=rawCd4DnaseI, subset=chrom %in%
+   c("chr1", "chr10", "chr19", "chr20"), scales=list(x=list(relation="free"))) 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>