labeled GRanges with ChromHMM chromatin states for GM12878

Description

labeled GRanges with ChromHMM chromatin states for GM12878

Usage

data(hmm878)

Format

The format is:
Formal class 'GRanges' [package "GenomicRanges"] with 6 slots
..@ seqnames :Formal class 'Rle' [package "IRanges"] with 4 slots
.. .. ..@ values : Factor w/ 23 levels "chr1","chr2",..: 1 2 3 4 5 6 7 8 9 10 ...
.. .. ..@ lengths : int [1:23] 54467 46499 37617 25155 30071 34846 29420 24506 24123 27263 ...
.. .. ..@ elementMetadata: NULL
.. .. ..@ metadata : list()
..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots
.. .. ..@ start : int [1:571339] 10001 10601 11138 11738 11938 12138 14538 20338 22138 22938 ...
.. .. ..@ width : int [1:571339] 600 537 600 200 200 2400 5800 1800 800 4000 ...
.. .. ..@ NAMES : NULL
.. .. ..@ elementType : chr "integer"
.. .. ..@ elementMetadata: NULL
.. .. ..@ metadata : list()
..@ strand :Formal class 'Rle' [package "IRanges"] with 4 slots
.. .. ..@ values : Factor w/ 3 levels "+","-","*": 3
.. .. ..@ lengths : int 571339
.. .. ..@ elementMetadata: NULL
.. .. ..@ metadata : list()
..@ elementMetadata:Formal class 'DataFrame' [package "IRanges"] with 6 slots
.. .. ..@ rownames : NULL
.. .. ..@ nrows : int 571339
.. .. ..@ listData :List of 4
.. .. .. ..$ name : chr [1:571339] "15_Repetitive/CNV" "13_Heterochrom/lo" "8_Insulator" "11_Weak_Txn" ...
.. .. .. ..$ score : num [1:571339] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. ..$ itemRgb: chr [1:571339] "#F5F5F5" "#F5F5F5" "#0ABEFE" "#99FF66" ...
.. .. .. ..$ thick :Formal class 'IRanges' [package "IRanges"] with 6 slots
.. .. .. .. .. ..@ start : int [1:571339] 10001 10601 11138 11738 11938 12138 14538 20338 22138 22938 ...
.. .. .. .. .. ..@ width : int [1:571339] 600 537 600 200 200 2400 5800 1800 800 4000 ...
.. .. .. .. .. ..@ NAMES : NULL
.. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. ..@ elementType : chr "ANY"
.. .. ..@ elementMetadata: NULL
.. .. ..@ metadata : list()
..@ seqinfo :Formal class 'Seqinfo' [package "GenomicRanges"] with 4 slots
.. .. ..@ seqnames : chr [1:23] "chr1" "chr2" "chr3" "chr4" ...
.. .. ..@ seqlengths : int [1:23] 249250621 243199373 198022430 191154276 180915260 171115067 159138663 146364022 141213431 135534747 ...
.. .. ..@ is_circular: logi [1:23] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. ..@ genome : chr [1:23] "hg19" "hg19" "hg19" "hg19" ...
..@ metadata :List of 1
.. ..$ url: chr "http://genome.ucsc.edu/cgi-bin/hgFileUi?g=wgEncodeBroadHmm&db=hg19"

Details

acquired using rtracklayer import from the bed file given at metadata(hmm878)[["url"]]

Source

see details

References

Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol. 2010 Aug;28(8):817-25.

Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011 May 5;473(7345):43-9.

Examples

data(hmm878)
table(hmm878$name)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GGtools)
Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Loading required package: data.table
Loading required package: parallel
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics

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: 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: 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


Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene

Attaching package: 'GGtools'

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

    getCall

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GGtools/hmm878.Rd_%03d_medium.png", width=480, height=480)
> ### Name: hmm878
> ### Title: labeled GRanges with ChromHMM chromatin states for GM12878
> ### Aliases: hmm878
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(hmm878)
> table(hmm878$name)

10_Txn_Elongation       11_Weak_Txn      12_Repressed 13_Heterochrom/lo 
            26509             82312             25483             75112 
14_Repetitive/CNV 15_Repetitive/CNV 1_Active_Promoter   2_Weak_Promoter 
             8028              6128             15278             35065 
3_Poised_Promoter 4_Strong_Enhancer 5_Strong_Enhancer   6_Weak_Enhancer 
             5263             25486             38604             69111 
  7_Weak_Enhancer       8_Insulator  9_Txn_Transition 
           109468             33265             16227 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>