[BioC] deepSNV error

[Julian Gehring]

Hi Asma,

The same as before, you need a 'GRanges' object, but supply a 
'GRangesList'.  See Dario's first answer to your post.

Best wishes
Julian


On 01.08.2014 04:43, Asma rabe wrote:
> 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 at 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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