[BioC] Combining two CompressedNormalIRangesList objects doesn't work

[Steve Lianoglou]

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