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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