---------- Forwarded message ---------- From: Asma rabe <asma.rabe@gmail.com> Date: Thu, Jul 31, 2014 at 2:42 PM Subject: Re: [BioC] deepSNV error To: Dario Strbenac <dstr7320@uni.sydney.edu.au> Hi Dario, Thank you very much. when i try only one exon or when i try a data frame of exons i got all counts =zero. I am sure that the input bam file can give a result what might be the problem?? #-------Using one exon dpSNV<-deepSNV(test="test.sorted.bam",control="control.sorted.bam",reg ions=gr[[3]],combine.method="fisher") > control(dpSNV)[1:3,] A T C G - a t c g _ [1,] 0 0 0 0 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 0 0 0 0 c<-control(dpSNV) > c[c>0] numeric(0) > t<-test(dpSNV) > t[t>0] numeric(0) #=============using many exons in a data frame library("TxDb.Hsapiens.UCSC.hg19.knownGene") txdb<-TxDb.Hsapiens.UCSC.hg19.knownGene tx_Exons<-exonsBy(txdb) gr<-tx_Exons[1:3] #Granges object #Data frame gr2<-as.data.frame(tx_Exons[1:300])[,2:4] #use 300 exons colnames(gr2)<-c("chr","start","stop") dpSNV1<-deepSNV(test="test.sorted.bam",control="control.sorted.bam",re gions=gr2,combine.method="fisher") all counts are zero as above. Any idea?? Thank you again for kind help. On Thu, Jul 31, 2014 at 11:00 AM, Dario Strbenac <dstr7320@uni.sydney.edu.au> wrote: > Hello, > > The error message is clear. You need to provide a GRanges or data.frame > variable for the regions of interest. If you read about exonsBy by opening > the help page using ?exonsBy, you will see the returned variable is a > GRangesList. Changing it to regions = gr[[1]] would test each exon of the > first transcript in the GRangesList. > > -------------------------------------- > Dario Strbenac > PhD Student > University of Sydney > Camperdown NSW 2050 > Australia > _______________________________________________ > 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]]

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]]