List of found ChIP-enriched regions

Description

This is the list of found ChIP-enriched regions. The package contains all the data to recreate the list and this list is merely given for convenience sake.

Usage

data(chersX)

Format

A cherList, a list of cher objects.

See Also

cher-class

Examples

data(chersX)
head(chersX)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(ccTutorial)
Loading required package: Ringo
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: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: Matrix
Loading required package: grid
Loading required package: lattice
Loading required package: affy

Attaching package: 'affy'

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

    probes

Loading required package: topGO
Loading required package: graph
Loading required package: GO.db
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


Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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

    members

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

    depth

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ccTutorial/chersX.Rd_%03d_medium.png", width=480, height=480)
> ### Name: chersX
> ### Title: List of found ChIP-enriched regions
> ### Aliases: chersX
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(chersX)
> head(chersX)
[[1]]
brain.H3K4me3.brain.smoothed.chr10.cher1 
Chr 10 : 3133434 - 3137470 
Antibody : H3K4me3.brain.smoothed 
Maximum level = 3.239658 
Score = 54.68394 
Spans 39 probes.
Defined extras: typeUpstream, typeInside, distMid2TSS, upSymbol, inSymbol, type 

[[2]]
brain.H3K4me3.brain.smoothed.chr10.cher2 
Chr 10 : 4521828 - 4523128 
Antibody : H3K4me3.brain.smoothed 
Maximum level = 2.531689 
Score = 11.80016 
Spans 14 probes.
Defined extras: typeUpstream, typeInside, distMid2TSS, upSymbol, inSymbol, type 

[[3]]
brain.H3K4me3.brain.smoothed.chr10.cher3 
Chr 10 : 4539730 - 4541606 
Antibody : H3K4me3.brain.smoothed 
Maximum level = 2.159177 
Score = 12.05056 
Spans 19 probes.
Defined extras: typeUpstream, typeInside, distMid2TSS, upSymbol, inSymbol, type 

[[4]]
brain.H3K4me3.brain.smoothed.chr10.cher4 
Chr 10 : 4795800 - 4797168 
Antibody : H3K4me3.brain.smoothed 
Maximum level = 2.859851 
Score = 14.19252 
Spans 14 probes.
Defined extras: typeUpstream, typeInside, distMid2TSS, upSymbol, inSymbol, type 

[[5]]
brain.H3K4me3.brain.smoothed.chr10.cher5 
Chr 10 : 4978328 - 4979728 
Antibody : H3K4me3.brain.smoothed 
Maximum level = 2.12597 
Score = 8.348753 
Spans 15 probes.
Defined extras: typeUpstream, typeInside, distMid2TSS, upSymbol, inSymbol, type 

[[6]]
brain.H3K4me3.brain.smoothed.chr10.cher6 
Chr 10 : 5151612 - 5152650 
Antibody : H3K4me3.brain.smoothed 
Maximum level = 2.563474 
Score = 9.532152 
Spans 10 probes.
Defined extras: typeUpstream, typeInside, distMid2TSS, upSymbol, inSymbol, type 

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>