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Jim Nemesh
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10
@jim-nemesh-4027
Last seen 10.4 years ago
Hi! I apologize if this is the wrong place to post a bug report - the
maintainer of the package is listed as: Maintainer Biocore Team c/o
BioC user list
I have a small set of range info:
start=c(187592960,246804638,193202778,151026713,150822234)
end=c(187810199,246862141,193212714,151037738,150856715)
mapRanges<-IRanges(start, end)
tree<-IntervalTree(mapRanges)
If I search the data against itself like this:
result=overlap(tree, mapRanges)@matchMatrix
query subject
[1,] 5 5
[2,] 4 4
[3,] 1 1
[4,] 3 3
[5,] 2 2
You can see each query matches only the subject - all is well in the
world so far.
But, if you do it this way:
result2=overlap(tree)
An object of class RangesMatching
Slot "matchMatrix":
query subject
[1,] 1 5
[2,] 2 4
[3,] 3 1
[4,] 4 3
[5,] 5 2
It looks item 1 is matching up to item 5, etc. Not so great.
if we sort the data first:
start=sort(start)
end=sort(end)
mapRanges<-IRanges(start, end)
tree<-IntervalTree(mapRanges)
result2=overlap(tree)
> result2
An object of class RangesMatching
Slot "matchMatrix":
query subject
[1,] 1 1
[2,] 2 2
[3,] 3 3
[4,] 4 4
[5,] 5 5
Things are once again right in the world.
I can't find anywhere in the documents where sorting is a requirement
to sort data when using a self-referential search. Is this a bug in
the documentation, or in the code itself? I would assume that the
IntervalTree class would perform sorting if it's a requirement for the
code to work correctly.
Otherwise, fantastic package that's saved me quite a bit of time.
Thanks
-Jim Nemesh
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