Entering edit mode
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
