CpG islands found by Wu, Irizarry, and Feinberg via hidden Markov model

Description

This GRanges object was constructed from the data provided at http://rafalab.jhsph.edu/CGI/model-based-cpg-islands-hg18.txt

Additional species and software to run the model can be found at http://rafalab.jhsph.edu/CGI/index.html

Author(s)

Tim Triche, Jr. (with data from Wu, Irizarry, and Feinberg)

Examples

  data(hg18.islands)
  split(hg18.islands, seqnames(hg18.islands))

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(FDb.InfiniumMethylation.hg18)
Loading required package: GenomicFeatures
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: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
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: TxDb.Hsapiens.UCSC.hg18.knownGene
Loading required package: org.Hs.eg.db

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/FDb.InfiniumMethylation.hg18/hg18.islands.Rd_%03d_medium.png", width=480, height=480)
> ### Name: hg18.islands
> ### Title: CpG islands found by Wu, Irizarry, and Feinberg via hidden
> ###   Markov model
> ### Aliases: hg18.islands
> ### Keywords: data
> 
> ### ** Examples
> 
> 
>   data(hg18.islands)
>   split(hg18.islands, seqnames(hg18.islands))
GRangesList object of length 47:
$chr1 
GRanges object with 4879 ranges and 3 metadata columns:
        seqnames                 ranges strand |  CpGcount     pctGC    obsExp
           <Rle>              <IRanges>  <Rle> | <integer> <numeric> <numeric>
  26739     chr1       [   497,   1104]      * |        77     0.712     1.018
  26740     chr1       [ 18599,  19664]      * |       115     0.734     0.823
  26741     chr1       [124949, 125696]      * |        44     0.676     0.548
  26742     chr1       [126027, 127119]      * |        66     0.694     0.534
  26743     chr1       [127521, 127984]      * |        24     0.662     0.504
    ...      ...                    ...    ... .       ...       ...       ...
  31613     chr1 [247119079, 247120082]      * |        81     0.656      0.75
  31614     chr1 [247123985, 247124241]      * |        21     0.689      0.69
  31615     chr1 [247134056, 247134227]      * |        15     0.622     0.902
  31616     chr1 [247134368, 247135235]      * |        56     0.545      0.87
  31617     chr1 [247166951, 247167602]      * |        78     0.729     0.973

...
<46 more elements>
-------
seqinfo: 47 sequences from an unspecified genome; no seqlengths
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> 
> dev.off()
null device 
          1 
>