Example 4C-seq data set of fetal liver data

Description

This data set contains an instance of a Data4Cseq object; 2185 reads on 453 fragments are included. Raw reads are mapped to fragments, but the read count has not yet been normalized.

The 4C-seq data was taken from Stadhouders et al's fetal liver data set.

Usage

  data("liverDataRaw")

Format

Formal class 'Data4Cseq'

Source

Shortened version of Stadhouders et al's fetal liver data:

Stadhouders, R., Thongjuea, S., et al. (2012): Dynamic long-range chromatin interactions control Myb proto-oncogene transcription during erythroid development. EMBO, 31, 986-999.

Examples

  data("liverDataRaw")
  liverDataRaw

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(Basic4Cseq)
Loading required package: Biostrings
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: XVector
Loading required package: GenomicAlignments
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
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")'.

Loading required package: Rsamtools
Loading required package: caTools

Attaching package: 'caTools'

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

    runmean

The following object is masked from 'package:S4Vectors':

    runmean

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Basic4Cseq/liverDataRaw.Rd_%03d_medium.png", width=480, height=480)
> ### Name: liverDataRaw
> ### Title: Example 4C-seq data set of fetal liver data
> ### Aliases: liverDataRaw
> ### Keywords: datasets
> 
> ### ** Examples
> 
>   data("liverDataRaw")
>   liverDataRaw
4C-seq experiment data
Type: Data4Cseq 
Viewpoint:  10 : 20879870 - 20882209 
Read length:  54 
Number of reads:  2185 
Number of total fragments:  453 
Number of near-cis fragments:  90 
Points of interest:  2 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>