DMRcaller calling duplicated/overlapping DMRs in bins mode
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@martingroth-22743
Last seen 2.4 years ago

Hi, I realised some inconsistencies when calling DMRs with the bins method of the computeDMRs function: some of the DMRs were duplicated and some were overlapping, even after merging them with the mergeDMRsIteratively function. Moreover, the output of compute DMRs differed when using cores=1 or cores=3. As a result genome coverage of the identified DMRs was much higher than with other DMR callers. To make sure that there is nothing wrong with my input data or installation, I repeated the examples from the vignette and found the same problems. This is even visible in the printed output in the vignette:

> print(DMRsBinsCG)
GRanges object with 40 ranges and 11 metadata columns:
       seqnames        ranges strand | sumReadsM1 sumReadsN1       proportion1 sumReadsM2 sumReadsN2          proportion2 cytosinesCount
          <Rle>     <IRanges>  <Rle> |  <numeric>  <numeric>         <numeric>  <numeric>  <numeric>            <numeric>      <numeric>
   [1]     Chr3 503000-503199      * |        299        731 0.409028727770178          1        776  0.00128865979381443             17
   [2]     Chr3 503100-503199      * |         13         28 0.464285714285714          0        100                    0              4
   [3]     Chr3 503400-503499      * |        158        198 0.797979797979798          0        414                    0             12
   [4]     Chr3 503400-504499      * |        959       1674 0.572879330943847          3       3183 0.000942507068803016             90
   [5]     Chr3 506400-506699      * |        182        321 0.566978193146417          3        546  0.00549450549450549             18
   ...      ...           ...    ... .        ...        ...               ...        ...        ...                  ...            ...
  [36]     Chr3 593700-594399      * |        660       1151 0.573414422241529          7       1907  0.00367068694284216             44
  [37]     Chr3 599000-599299      * |         77        184 0.418478260869565          3        356  0.00842696629213483             14
  [38]     Chr3 599200-599299      * |         20         35 0.571428571428571          0        107                    0              6
  [39]     Chr3 599500-599599      * |        168        219 0.767123287671233          0        201                    0              8
  [40]     Chr3 599500-599599      * |        168        219 0.767123287671233          0        201                    0              8
           context direction                        pValue  regionType
       <character> <numeric>                     <numeric> <character>
   [1]          CG        -1          4.74722531863148e-87        loss
   [2]          CG        -1 0.000000000000654240817434598        loss
   [3]          CG        -1          1.65931737416942e-98        loss
   [4]          CG        -1                             0        loss
   [5]          CG        -1          2.63625235917949e-84        loss
   ...         ...       ...                           ...         ...
  [36]          CG        -1         2.64404156484762e-298        loss
  [37]          CG        -1          5.89784614791408e-37        loss
  [38]          CG        -1          3.36772077461907e-17        loss
  [39]          CG        -1          1.19820628741886e-57        loss
  [40]          CG        -1          1.19820628741886e-57        loss
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

E.g. ranges 3 and 4 are overlapping, and ranges 39 and 40 are duplicated.

Any ideas what might be the problem? Thanks in advance!

DMRcaller • 215 views
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