How to get the all CpG sites genome postion for hg19
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@ericotorrieri-12900
Last seen 6.9 years ago
I want to find all CpG sites coordinates of hg19, could you give me any suggestions?
CpG • 5.8k views
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@james-w-macdonald-5106
Last seen 14 hours ago
United States

CpG sites, or CpG islands? You can get the islands from UCSC, most easily from AnnotationHub

> library(AnnotationHub)
> hub <- AnnotationHub()
updating metadata: retrieving 1 resource
  |======================================================================| 100%
snapshotDate(): 2016-10-11
> query(hub, c("cpg","hg19"))
AnnotationHub with 2 records
# snapshotDate(): 2016-10-11
# $dataprovider: UCSC
# $species: Homo sapiens
# $rdataclass: GRanges
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH5086"]]'

           title      
  AH5086 | CpG Islands
  AH5096 | Evo Cpg  

 
> cpgs <- hub[["AH5086"]]
downloading from 'https://annotationhub.bioconductor.org/fetch/5086'
retrieving 1 resource
  |======================================================================| 100%
> cpgs
GRanges object with 28691 ranges and 1 metadata column:
                       seqnames           ranges strand |        name
                          <Rle>        <IRanges>  <Rle> | <character>
      [1]                  chr1 [ 28736,  29810]      * |    CpG:_116
      [2]                  chr1 [135125, 135563]      * |     CpG:_30
      [3]                  chr1 [327791, 328229]      * |     CpG:_29
      [4]                  chr1 [437152, 438164]      * |     CpG:_84
      [5]                  chr1 [449274, 450544]      * |     CpG:_99
      ...                   ...              ...    ... .         ...
  [28687]  chr9_gl000201_random [ 15651,  15909]      * |     CpG:_30
  [28688]  chr9_gl000201_random [ 26397,  26873]      * |     CpG:_43
  [28689] chr11_gl000202_random [ 16284,  16540]      * |     CpG:_23
  [28690] chr17_gl000204_random [ 54686,  57368]      * |    CpG:_228
  [28691] chr17_gl000205_random [117501, 117801]      * |     CpG:_23
  -------
  seqinfo: 93 sequences (1 circular) from hg19 genome

If you mean the actual positions of all CpG sites, then you could use a modification of code posted on this site about 6 years ago, by Aaron Statham How to get the all CpG sites genome postion for mm9?.

> library(BSgenome.Hsapiens.UCSC.hg19)  
> chrs <- names(Hsapiens)[1:24]
> cgs <- lapply(chrs, function(x) start(matchPattern("CG", Hsapiens[[x]])))

> cpgr <- do.call(c, lapply(1:24, function(x) GRanges(names(Hsapiens)[x], IRanges(cgs[[x]], width = 2))))
There were 23 warnings (use warnings() to see them)
> cpgr
GRanges object with 28217009 ranges and 0 metadata columns:
             seqnames               ranges strand
                <Rle>            <IRanges>  <Rle>
         [1]     chr1       [10469, 10470]      *
         [2]     chr1       [10471, 10472]      *
         [3]     chr1       [10484, 10485]      *
         [4]     chr1       [10489, 10490]      *
         [5]     chr1       [10493, 10494]      *
         ...      ...                  ...    ...
  [28217005]     chrY [59362433, 59362434]      *
  [28217006]     chrY [59362485, 59362486]      *
  [28217007]     chrY [59362488, 59362489]      *
  [28217008]     chrY [59362493, 59362494]      *
  [28217009]     chrY [59362591, 59362592]      *
  -------
  seqinfo: 24 sequences from an unspecified genome; no seqlengths
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