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 Mu?oz Torres skype: pau_marc http://www.linkedin.com/in/paumarc http://www.researchgate.net/profile/Pau_Marc_Torres3/info/