motifs order on importing the motifs from bigWig file
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@stefandvoretskii-16727
Last seen 3.9 years ago

We have a GRanges object with motifs of interest:

 

>motifs_gr
GRanges object with 78181 ranges and 1 metadata column:
          seqnames              ranges strand |    regionID
             <Rle>           <IRanges>  <Rle> | <character>
      [1]     chr1       829075-829135      + |       donor
      [2]     chr1       847777-847837      + |       donor
      [3]     chr1       849573-849633      + |       donor
      [4]     chr1       852081-852141      + |       donor
      [5]     chr1       852737-852797      + |       donor
      ...      ...                 ...    ... .         ...
  [78177]     chrX 155334340-155334400      - |       donor
  [78178]     chrX 155513955-155514015      - |       donor
  [78179]     chrX 155524425-155524485      - |       donor
  [78180]     chrX 155545065-155545125      - |       donor
  [78181]     chrX 155612761-155612821      - |       donor
  -------
  seqinfo: 23 sequences from an unspecified genome; no seqlengths

We import the scores from BigWigFile like this:

gr_frq_mtx = import.bw(snakemake@input[['g1000SNPTrack']], which = motifs_gr, 
                          as = 'NumericList')%>%as.matrix

It turns out that the indexes of the resulting matrix do not match those of original GRanges objects (i.e., n-th row of the matrix does not necessarilly represent the n-th motif in GRanges). For us it is very important though. How could one overcome that?

 

Thanks in advance,

Stefan.

R rtracklayer data import • 466 views
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@michael-lawrence-3846
Last seen 9 months ago
United States

This could be improved, but as it is, there are two options:

  1. Ensure that the GRanges is sorted by the seqlevels as they are in the BigWig file.
  2. The resulting NumericList contains a metadata() field named "ranges", which is the which ranges in the order of the result.
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