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Question: How can I annotate GRanges object in R with refSeqID, gene symbol, description and entrezID?
1
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I have GRanges object which i got from methylKit. It looks like

GRanges with 148 ranges and 2 metadata columns:
        seqnames                 ranges strand   |               qvalue
           <Rle>              <IRanges>  <Rle>   |            <numeric>
    [1]     chr1   [ 1173916,  1174263]      *   | 9.62686423555631e-08
    [2]     chr1   [ 2121018,  2121818]      *   |                    0
    [3]     chr1   [ 7887199,  7887476]      *   |                    0
    [4]     chr1   [27675920, 27678016]      *   |                    0
    [5]     chr1   [38461585, 38461988]      *   |                    0
    ...      ...                    ...    ... ...                  ...
  [144]     chr9 [140310895, 140312457]      *   |                    0
  [145]     chrX [ 12601483,  12601832]      *   |                    0
  [146]     chrX [ 44169511,  44169765]      *   |                    0
  [147]     chrX [153193514, 153194074]      *   |                    0
  [148]     chrY [ 13370337,  13370718]      *   |                    0
                meth.diff
                <numeric>
    [1] -18.3771706593283
    [2]  17.4420646973258
    [3] -27.3603533740319
    [4]  23.8514605550414
    [5]  22.0042776419856
    ...               ...
  [144]  36.7176878762224
  [145]  16.0299020341895
  [146]  31.7676985330744
  [147]   20.503021579582
  [148]  16.6634521596941
  ---
  seqlengths:
    chr1 chr10 chr11 chr12 chr13 chr14 ...  chr6  chr7  chr8  chr9  chrX  chrY
      NA    NA    NA    NA    NA    NA ...    NA    NA    NA    NA    NA    NA

How can I annotate it with with refSeqID, gene symbol, description and entrezID?

ADD COMMENTlink 4.7 years ago Tori • 80 • updated 4.7 years ago Na Sed • 280
2
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Please see here.

Maybe it solves your problem.

ADD COMMENTlink 4.7 years ago Na Sed • 280

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