Entering edit mode
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.