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. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

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. >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >