Hi Dario,Bioconductors,


Thank you very much Dario for help.


When i try using loadAllData in deepSNV package ,i got an error. below is
script and error:


#=====================

library("TxDb.Hsapiens.UCSC.hg19.knownGene")

txdb<-TxDb.Hsapiens.UCSC.hg19.knownGene

tx_Exons<-exonsBy(txdb)


gr<-tx_Exons[1]


files<-c("test.sorted.bam","control.sorted.bam")

counts<-loadAllData(files,gr,q=10)

#------------------

Error in unlist(sapply(1:nrow(regions), function(i) rep(regions$chr[i],  :

  error in evaluating the argument 'x' in selecting a method for function
'unlist': Error in 1:nrow(regions) : argument of length 0

#=====================


Any idea??



On Thu, Jul 31, 2014 at 4:00 PM, Dario Strbenac <dstr7320@uni.sydney.edu.au>
wrote:

> If you put the BAM file into a genome browser, such as IGV, are there any
> reads overlapping that exon ? You only had a look at one exon. Not all
> exons will have reads in them.
>
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