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Adding gene to GRange objects with single base

Hi all,

I have a Grange objects look like this:

GRanges object with 4598553 ranges and 2 metadata columns:
          seqnames    ranges strand |         ref         alt
             <Rle> <IRanges>  <Rle> | <character> <character>
        1     chr1     51479      * |           T           A
        2     chr1     51803      * |           T           C
        3     chr1     52238      * |           T           G
        4     chr1     54490      * |           G           A
        5     chr1     54712      * |   TTTTCTTTC           T

and a bed files in Grange:

GRanges object with 57736 ranges and 1 metadata column:
          seqnames            ranges strand |   gene_name
             <Rle>         <IRanges>  <Rle> | <character>
      [1]        1       11869-14412      * |     DDX11L1
      [2]        1       14363-29806      * |      WASH7P
      [3]        1       29554-31109      * |  MIR1302-10
      [4]        1       34554-36081      * |     FAM138A
      [5]        1       52473-54936      * |      OR4G4P
      ...      ...               ...    ... .         ...

How can I merge two Grange objects so that I can know which SNP is belongs to which genes, for e.g: from this post

GRanges object with 4 ranges and 1 metadata column:
      seqnames    ranges strand |       names
         <Rle> <IRanges>  <Rle> | <character>
  [1]        I       1-3      * |   ENS001912
  [2]        I       6-8      * |        <NA>
  [3]        I     11-13      * |   ENS003901
  [4]        I     16-18      * |        <NA>
granges genomics
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updated by ATpoint ATpoint • written by QX • QX

Use findOverlaps but be sure that the chromosome identifiers are the same. Here you have 1, chr1 and I all three mixed.

• 0 views • link
written by ATpoint ATpoint

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