A test ChIP-Seq dataset

Description

A small subset of a ChIP-Seq dataset downloaded from the Short-Read Archive.

Usage

data(cstest)

Format

The dataset is on object of class GRangesList with read alignments from three chromosomes in two lanes representing CTCF and GFP pull-down in mouse.

Source

Short Read Archive, GEO accession number GSM288351 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM288351

References

Chen X., Xu H., Yuan P., Fang F., Huss M., Vega V.B., Wong E., Orlov Y.L., Zhang W., Jiang J., Loh Y.H., Yeo H.C., Yeo Z.X., Narang V., Govindarajan K.R., Leong B., Shahab A.S., Ruan Y., Bourque G., Sung W.K., Clarke N.D., Wei C.L., Ng H.H. (2008), “Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells”. Cell, 133:1106-1117.

Examples

data(cstest)
names(cstest)
cstest$gfp

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(chipseq)
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

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: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: XVector
Loading required package: Rsamtools
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

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

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/chipseq/cstest.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cstest
> ### Title: A test ChIP-Seq dataset
> ### Aliases: cstest
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(cstest)
> names(cstest)
[1] "ctcf" "gfp" 
> cstest$gfp
GRanges object with 295385 ranges and 0 metadata columns:
           seqnames                 ranges strand
              <Rle>              <IRanges>  <Rle>
       [1]    chr10     [3002512, 3002535]      +
       [2]    chr10     [3009093, 3009116]      +
       [3]    chr10     [3020716, 3020739]      +
       [4]    chr10     [3023026, 3023049]      +
       [5]    chr10     [3024629, 3024652]      +
       ...      ...                    ...    ...
  [295381]    chr12 [121213126, 121213149]      -
  [295382]    chr12 [121216905, 121216928]      -
  [295383]    chr12 [121216967, 121216990]      -
  [295384]    chr12 [121251805, 121251828]      -
  [295385]    chr12 [121253426, 121253449]      -
  -------
  seqinfo: 35 sequences from an unspecified genome
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>