Transform genomic intervals to genomic positions in an R dataframe
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2.5 years ago
jeni ▴ 60

Hi everyone!

I have a dataframe with some genomic intervals and its corresponding coverage in several samples:

            sample1  sample2   sample3
     1:1-3    30        NA      NA
     1:1-4    NA        40      35
     1:4-5    35        NA      NA
     1:5-7    NA        50      50
     1:6-7    60        NA      NA

I would like to obtain the same dataframe but for genomic positions:

            sample1    sample2     sample3
     1:1      30         40          35
     1:2      30         40          35
     1:3      30         40          35
     1:4      35         40          35
     1:5      35         50          50 
     1:6      60         50          50
     1:7      60         50          50

How could I get this?

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The intervals can be obtained first by rownames. Then use strsplit to get the chromosome (first element) and the ranges (2nd and 3rd element). You can either put this into a data frame and use then makeGRangesFromDataFrame or use GRanges directly to construct a GRanges object. The coverages could be stored as elementMetadata in the resulting GRanges object. I suggest you try that out. It is a good practice to improve yourself.

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Okay, thanks! I have already done that.

But now how can I get genomic positions from each interval, indicating the coverage value of each sample for each position?

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Can you show what you have done?

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Sure! I've transformed my dataframe in a GRanges object (I've splitted first genomic coordinates to this format -> chr start end):

gr<-makeGRangesFromDataFrame(df, seqnames.field = 'chrm', start.field = 'start', end.field = 'end', keep.extra.columns = TRUE)

GRanges object with 5 ranges and 3 metadata columns:
      seqnames    ranges strand |     sample1     sample2     sample3
         <Rle> <IRanges>  <Rle> | <character> <character> <character>
  [1]        1       1-3      * |          30          NA          NA
  [2]        1       1-4      * |          NA          40          35
  [3]        1       4-5      * |          35          NA          NA
  [4]        1       5-7      * |          NA          50          50
  [5]        1       6-7      * |          60          NA          NA
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

Now, I have tried:

grd<-disjoin(gr)

and I get this:

GRanges object with 4 ranges and 0 metadata columns:
      seqnames    ranges strand
         <Rle> <IRanges>  <Rle>
  [1]        1       1-3      *
  [2]        1         4      *
  [3]        1         5      *
  [4]        1       6-7      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

In this example I cannot obtain all the positions, but in my real df I can, because I have a lot of overlapped intervals. Now the problem I have is that I dont know how to maintain and adapt metadata columns, what I would like is to obtain this:

GRanges object with 4 ranges and 3 metadata columns:
      seqnames    ranges strand   |   sample1 sample2 sample3
         <Rle> <IRanges>  <Rle>   |  character  character character
  [1]        1       1-3      *                |      30              40            35
  [2]        1         4      *                 |      35              40            35
  [3]        1         5      *                 |      35              50            50
  [4]        1       6-7      *                |      60              50            50
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