---------- 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",regions=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",regions=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
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