[BioC] subset a RleList using GRanges object?

[Hervé Pagès]

Hi Michael,

On 12/03/2013 07:13 PM, Michael Lawrence wrote:
> For now, just coerce to a RangesList.
>
> z [ as(myRange, "RangesList") ]
>
> Herve might consider adding a [,List,GenomicRanges method... kind of a
> logical leap though from seqnames to list element names.

This is something I've been considering for a while. I think we should
do it. The mapping between the seqnames of a GRanges and the names of a
RangesList is well established at this point e.g. the coercion (back and
forth) between the two already does that.

Cheers,
H.

>
> extractCoverageForPositions is different; it extracts an integer vector
> given a vector of width-one positions.
>
>
>
>
>
>
> On Tue, Dec 3, 2013 at 4:53 PM, Janet Young <jayoung at fhcrc.org> wrote:
>
>> Hi there,
>>
>> I'm playing around with coverage data generated outside of R, planning to
>> plot RNA-seq coverage for some genes we're interested in.
>>
>> I have a request - it'd be nice from my point of view if it were possible
>> to look at a small region an RleList (or CompressedRleList) using a GRanges
>> object to focus on that smaller region.  Looks like I can subset a single
>> Rle object with an IRanges object, but I wonder if this nice feature could
>> be extended to GRanges objects?
>>
>> Some code is below to show what I'm trying to do.
>>
>> thanks veruy much,
>>
>> Janet
>>
>>
>>
>> library(GenomicRanges)
>>
>> ## an example RleList
>> x <- Rle(10:1, 1:10)
>> y <- Rle(10:1, 1:10)
>> z <- RleList( chr1=x, chr2=y)
>>
>> ## an example GRanges object
>> myRange <- GRanges( seqnames="chr1", ranges=IRanges(start=10,end=15) )
>>
>> ## subsetting an Rle using an IRanges object works, as expected:
>> z[["chr1"]] [ ranges(myRange) ]
>>
>> ## but subsetting an RleList by GRanges object doesn't work
>> z [ myRange ]
>> # Error in normalizeSingleBracketSubscript(i, x) : invalid subscript type
>>
>> sessionInfo()
>>
>> R Under development (unstable) (2013-11-06 r64163)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>> [1] GenomicRanges_1.15.10 XVector_0.3.2         IRanges_1.21.13
>> [4] BiocGenerics_0.9.1
>>
>> loaded via a namespace (and not attached):
>> [1] stats4_3.1.0
>>
>>
>>
>>
>> -------------------------------------------------------------------
>>
>> Dr. Janet Young
>>
>> Malik lab
>> http://research.fhcrc.org/malik/en.html
>>
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Avenue N., A2-025,
>> P.O. Box 19024, Seattle, WA 98109-1024, USA.
>>
>> tel: (206) 667 4512
>> email: jayoung  ...at...  fhcrc.org
>>
>> -------------------------------------------------------------------
>>
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>>
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

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