[BioC] Combining two CompressedNormalIRangesList objects doesn't work

[Steve Lianoglou]

Thanks for the fix.

It might be a while before I swap this back into my workflow, but I'll
let you know if I run into any walls.

-steve


On Tue, Oct 26, 2010 at 2:31 PM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> Thanks for looking into this Steve. The internals of IRanges are a dark and
> confusing place. I just committed a fix that simply has
> CompressedNormalIRangesLists keeping IRanges as its element type, not
> NormalIRanges, as it is not possible in general to compress the elements
> into a NormalIRanges.
>
> Let me know if this works for you,
> Michael
>
> On Sun, Oct 24, 2010 at 10:37 PM, Steve Lianoglou
> <mailinglist.honeypot at gmail.com> wrote:
>>
>> Sorry, forgot to attach the sessionInfo:
>>
>> R version 2.12.0 (2010-10-15)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-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] GenomicRanges_1.2.0 IRanges_1.8.0
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.12.0
>>
>>
>> On Mon, Oct 25, 2010 at 1:35 AM, Steve Lianoglou
>> <mailinglist.honeypot at gmail.com> wrote:
>> > I'm tripping up on this because I want to combine two GappedRanges
>> > objects, which essentially boils down to `c`(ombining)
>> > CompressedNormalIRangesList objects:
>> >
>> > R> irl <- new("CompressedIRangesList"
>> >    , elementMetadata = NULL
>> >    , elementType = "IRanges"
>> >    , metadata = list()
>> >    , partitioning = new("PartitioningByEnd"
>> >    , end = c(3L, 4L, 6L)
>> >    , NAMES = NULL
>> >    , elementMetadata = NULL
>> >    , elementType = "integer"
>> >    , metadata = list()
>> > )
>> >    , unlistData = new("IRanges"
>> >    , start = c(11L, 21L, 23L, -2L, -2L, 21L)
>> >    , width = c(5L, 1L, 8L, 18L, 13L, 2L)
>> >    , NAMES = NULL
>> >    , elementMetadata = NULL
>> >    , elementType = "integer"
>> >    , metadata = list()
>> > ))
>> >
>> > R> c(irl, irl) ## works
>> >
>> > R> cnirl <- as(irl, 'CompressedNormalIRangesList')
>> > R> c(cnirl, cnirl) ## error
>> > Error in newCompressedList(class(tls[[1L]]), unlistData, end =
>> > partitionEnd,  :
>> >  'unlistData' not of class NormalIRanges
>> >
>> > ## GappedRanges uses CompressedNormalIRangesList objects at its core
>> > ## and also fails
>> > R> g <- as(irl, 'GappedRanges')
>> > R> c(g, g)
>> > Error in newCompressedList(class(tls[[1L]]), unlistData, end =
>> > partitionEnd,  :
>> >  'unlistData' not of class NormalIRanges
>> >
>> > Being able to debug(IRanges:::newCompressedList), I can see that it
>> > expects to build "NormalIRanges" objects into a list since the value
>> > of `elementTypeData`` is "NormalIRanges", but the value of
>> > `unlistData` is simply an IRanges object, so the function fails by `if
>> > (!extends(class(unlistData), elementTypeData))` evaluating to TRUE,
>> > which then throws the error we see here.
>> >
>> > I've been chasing my tail for a bit trying to plumb the internals of
>> > the IRanges inheritance hierarchy to pinpoint the exact place I can
>> > make a change for this to work. I guess some special casing needs to
>> > be applied in this function, or the setMethod("c", "CompressedList")
>> > function to look for "NormalIRanges" objects, but I'm at a loss right
>> > now and running out of steam.
>> >
>> > Can anybody offer some insight/fix?
>> >
>> > Thanks,
>> > -steve
>> >
>> > --
>> > Steve Lianoglou
>> > Graduate Student: Computational Systems Biology
>> >  | Memorial Sloan-Kettering Cancer Center
>> >  | Weill Medical College of Cornell University
>> > Contact Info: http://cbio.mskcc.org/~lianos/contact
>> >
>>
>>
>>
>> --
>> Steve Lianoglou
>> Graduate Student: Computational Systems Biology
>>  | Memorial Sloan-Kettering Cancer Center
>>  | Weill Medical College of Cornell University
>> Contact Info: http://cbio.mskcc.org/~lianos/contact
>>
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>
>



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact