Question: Annotating and Visualizing methylation percentage data
1
gravatar for dBlandford
5.2 years ago by
dBlandford20
Israel
dBlandford20 wrote:

Hey,

I recently analyzed methylation data using the multtest bioconductor package, and have constructed a GRanges object using the results:

           seqnames               ranges strand   |            t.value     Bonfp
              <Rle>            <IRanges>  <Rle>   |          <numeric> <numeric>
       [1]     chr1       [10498, 10498]      *   | -0.259241494586852         1
       [2]     chr1       [11059, 11059]      *   |  0.741650220479654         1
       [3]     chr1       [11158, 11158]      *   |  0.436314460597879         1
       [4]     chr1       [11185, 11185]      *   |   0.56407885996267         1
       [5]     chr1       [11481, 11481]      *   |  0.448740908931989         1
       ...      ...                  ...    ... ...                ...       ...
  [234423]     chrY [59361545, 59361545]      *   |   0.56407885996267         1
  [234424]     chrY [59361572, 59361572]      *   |   0.53159181236817         1
  [234425]     chrY [59361674, 59361674]      *   |  0.960939343846552         1
  [234426]     chrY [59362174, 59362174]      *   | -0.955755883828529         1
  [234427]     chrY [59362341, 59362341]      *   | -0.450128953355832         1

Is there any way to get this data annotated? So far I just manually entered the position into UCSC for every significant value, but there must be a more efficent way. I tried to use solutions such as annotationhub or rtracklayer, but I think my data might be formatted improperly in some way?

Also, ignoring the annotation issue - is there any way to comfortably visualize this data? I'm searching for something similar to a manhattan plot, with -logp by pos/chr.

Thanks

ADD COMMENTlink written 5.2 years ago by dBlandford20
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