[Bioc-sig-seq] ScanBamParam suggestion

[Martin Morgan]

On 09/29/2011 05:26 PM, Janet Young wrote:
> Hi,
>
> I have a suggestion to make ScanBamParam easier to use for coding
> amateurs like myself (I'm still sometimes confused with the many ways
> to encode genomic regions):
>
> Is it easy/possible to change bamWhich function to accept GRanges
> objects, rather than requiring RangesList?  See below...

yep, should be in 1.5.68 when it becomes available. Thanks for the 
suggestion. Martin

>
> thanks, as usual,
>
> Janet
>
>
>
> ############ library(Rsamtools) myGR<-
> GRanges(seqnames="chr1",ranges=IRanges(start=1,end=100))
>
> # I can use GRanges as the "which" argument if I do it when I create
> the ScanBamParam object myparams1<- ScanBamParam(which=myGR)
>
> #but not if I try to set later myparams2<- ScanBamParam()
> bamWhich(myparams2)<- myGR ### Error in checkSlotAssignment(object,
> name, value) : ###   assignment of an object of class "GRanges" is
> not valid for slot "which" ### in an object of class "ScanBamParam";
> is(value, "RangesList") is not TRUE
>
> ## it's OK, though coercion does work. bamWhich(myparams2)<-
> as(myGR,"RangesList")
>
> sessionInfo() R version 2.13.1 (2011-07-08) Platform:
> i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages: [1] stats     graphics  grDevices utils
> datasets  methods   base
>
> other attached packages: [1] Rsamtools_1.4.3     Biostrings_2.20.4
> GenomicRanges_1.4.8 IRanges_1.10.6
>
> ###########
>
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> mailing list Bioc-sig-sequencing at r-project.org
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