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Asked: 2026-06-16T03:15:23+00:00

The genoset R package has a function for building a GenoSet by putting together

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The genoset R package has a function for building a GenoSet by putting together several matrices and a RangedData object that specifies co-ordinates.

I have the following objects – three matrices, all with the same name, and a RangedData object of the following format (called locData).

               space                 ranges |
            <factor>              <IRanges> |
 cg00000957        1 [  5937253,   5937253] |
 cg00001349        1 [166958439, 166958439] |
 cg00001583        1 [200011786, 200011786] |
 cg00002028        1 [ 20960010,  20960010] |
 cg00002719        1 [169396706, 169396706] |
 cg00002837        1 [ 44513358,  44513358] |

When I try to create a GenoSet, though, I get the following error.

 DMRSet=GenoSet(locData,Exprs,meth,unmeth,universe=NULL)

Error in .Call2(“IRanges_from_integer”, from, PACKAGE = “IRanges”) :
cannot create an IRanges object from an integer vector with missing values.

What am I doing wrong? all the objects I’m putting together have the same rownames, except for the IRanges object itself, which I don’t think has rownames since it isn’t a matrix.
Additionally, the “column” of locData has non-integer characters.

Thank you!

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1 Answer

  1. Editorial Team

    It sounds like your "locData" may not be a RangedData. It can alternatively be a GRanges. Either way, you will want to name all of your arguments.

    The underlying eSet class will be upset about that once you get past the locData trouble.

    DMRSet=GenoSet(locData=locData,exprs=Exprs,meth=meth,unmeth=unmeth,universe=NULL)

    Pete

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