hmm878: labeled GRanges with ChromHMM chromatin states for GM12878

In gQTLstats: gQTLstats: computationally efficient analysis for eQTL and allied studies

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)

gQTLstats documentation built on Nov. 8, 2020, 7:53 p.m.