Deleted:goregion : Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'NSBS' for signature '"AsIs"'
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3.2 years ago
Basti ★ 2.0k

Hi,

I'm trying to perform GO using goregion on a Granges object obtained from extractRanges after using dmrcate and I can't find the solution to my problem.

enrichment_GO <- goregion(results.ranges,all.cpg=all, collection = "KEGG", array.type = "EPIC",plot.bias = TRUE, prior.prob = TRUE,)

All input CpGs are used for testing.
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'NSBS' for signature '"AsIs"'

results.ranges

GRanges object with 20566 ranges and 8 metadata columns:
          seqnames              ranges strand |   no.cpgs min_smoothed_fdr    Stouffer     HMFDR      Fisher      maxdiff     meandiff      overlapping.genes
             <Rle>           <IRanges>  <Rle> | <integer>        <numeric>   <numeric> <numeric>   <numeric>    <numeric>    <numeric>            <character>
      [1]    chr11     2321770-2324401      * |        36      1.82151e-38 9.77154e-28 0.0304349 1.67686e-20     0.158230    0.0997781 LSP1, TSPAN32, C11or..

 -------
  seqinfo: 24 sequences from an unspecified genome; no seqlengths

It seems this kind of error is common but I can't find the right solution for my case. Does anyone have an idea how to solve this ? Thanks.

R goregion GRanges • 898 views
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