Hello everybody,
I am using the library rapidr of bioconductor, I am running it without
problems as follows;
library("RAPIDR")
makeBinnedCountsFile("SRR611842_2.bam","SRR611842_2.bam.bai","binnecounts.r",mask=NULL,k=20000)
> SampleID=c("SRR611842_2")
> DX=c("T21")
> Gender=c("Male")
> frame= data.frame(SampleID, DX, Gender)
No problems until here , but when i do
> createReferenceSetFromCounts("binnecounts.r",frame)
Loading binned counts file
Checking every sampleID has an outcome
No outcomes for Sample SRR611842_2.bam.bai
*Error in `[.data.frame`(sampleIDs.with.outcomes, , "Gender") :*
* undefined columns selected*
I do not understand this error, it seems as if the column DX is not read by
the function and I do not know why. I have tried both spellings Dx and DX
with the same result.
I also cheked for the DX columns doing
> frame
SampleID DX Gender
1 SRR611842_2 T21 Male
> frame$DX
[1] T21
Levels: T21
> names(frame)
[1] "SampleID" "DX" "Gender"
Can anyone suggest me what to do?
Pau Marc Muñoz Torres
skype: pau_marc
http://www.linkedin.com/in/paumarc
http://www.researchgate.net/profile/Pau_Marc_Torres3/info/
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