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Question: "genomdat must be numeric" error form DNACopy package
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gravatar for perdomos
2.4 years ago by
perdomos0
France
perdomos0 wrote:

I am having trouble creating a CNA object from a oligoSnpSet matrix after applying the crlmm package

I keep getting "genomdat must be numeric" error from my

 

oligoset<- OligoSetList(cnSet3, batch.name=batch(cnSet3)[1])

oligo<-oligoset[[1]]

CNA.object <- CNA(genomdat=copyNumber(oligo),chrom=chromosome(oligo), maploc=position(oligo),data.type="logratio", sampleid = sampleNames(oligo))

ADD COMMENTlink modified 2.4 years ago by James W. MacDonald45k • written 2.4 years ago by perdomos0
0
gravatar for James W. MacDonald
2.4 years ago by
United States
James W. MacDonald45k wrote:

You haven't given enough information for anybody to help you, but there is likely enough information for you to help yourself.

Note the error says 'genomdat must be numeric', and there is a genomdat argument to CNA(). This indicates that at least some of the data you are passing in are not numeric. In addition, the help for copyNumber() says that genomdat has to be a vector or matrix. The obvious thing to do is to explore what you are passing in for the genomdat argument

genomdat <- copyNumber(oligo)

class(genomdat)

is.numeric(genomdat)

You may need to coerce the output of copyNumber() to the correct format for CNA().

 

ADD COMMENTlink written 2.4 years ago by James W. MacDonald45k
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