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Error running ExomeDepth

Hello I'm testing ExomeDepth and I'm doing the tutorial from ExomeDepth-vignette, when I'm creating my reference set I write:

my.choice<-select.reference.set(test.counts=my.matrix[,i],
                                  reference.counts= my.matrix[,-i],
                                  bin.length= (ExomeCount.dafr$end - ExomeCount.dafr$start)/1000,
                                  n.bins.reduced=1000)

Then I receive this message:

Error in my.matrix[, i] : index out of bounds.

Can anybody help me?

Thank you very much

exome r
• 2,822 views • link
updated by Ram Ram • written by BarbaraZ • BarbaraZ

What value is i and what are the dimensions of my.matrix?

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updated by Ram Ram • written by Devon Ryan Devon Ryan

my.matrix has 185130 rows and 0 columns and obviously nsamples is equal to 0.

I've tried to do the same thing with tutorial data and the result is the same

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updated by Ram Ram • written by BarbaraZ • BarbaraZ

Yeah, a 0-column matrix is empty, so that'll be your problem :)

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written by Devon Ryan Devon Ryan

Thank you very much for your help, I found the error

• 0 views • link
updated by Ram Ram • written by BarbaraZ • BarbaraZ

1 answer

I'm sorry, I'm wrong, the problem is only about my data, probably my dataset in not appropriate

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written by BarbaraZ • BarbaraZ

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