Data for vignette example 4.

Description

Broadpeaks file mapping H3K9me3 marks in human lymphoblastoid cells (peaks from chr1, chr2, and chrX).

Usage

data(GSM733664_broadPeaks)

Details

GEO accession GSM733664, subset containing chr1,chr2,and chrX peaks.

References

ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74.

Examples

data(GSM733664_broadPeaks)
head(GSM733664_broadPeaks)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(IdeoViz)
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: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: RColorBrewer
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/IdeoViz/GSM733664_broadPeaks.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GSM733664_broadPeaks
> ### Title: Data for vignette example 4.
> ### Aliases: GSM733664_broadPeaks
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(GSM733664_broadPeaks)
> head(GSM733664_broadPeaks)
  chrom chromStart chromEnd name score strand signalValue pValue qValue
1  chr1      10141    10374    .   993      .   10.796883   10.3     -1
2  chr1     567457   567702    .  1000      .   16.590333  100.0     -1
3  chr1     569826   570047    .  1000      .   15.757614  100.0     -1
4  chr1     723167   727602    .   808      .    8.389733   14.2     -1
5  chr1     816959   817136    .   793      .    8.188648    1.7     -1
6  chr1     821181   821421    .   753      .    7.660859    3.4     -1
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>