> One thing I’m not clear on is how to expand the ranges from one step
> to the next. The way GenomicInteractions are structured, there is a
> Granges object with all possible ranges, and the GInteractions object
> is populated by reference to said interactions.
If you're already in C++, then lif
Hi Luke,
If I understand correctly what you want to do, you can use `findOverlaps()`
to create a new GInteractions object from a set of expanded ranges and the
original interactions.
anchor.one <- GRanges(c("chr1", "chr1", "chr1", "chr1"),
IRanges(c(10, 20, 30, 20), width=5))
Thank you for the tip, Aaron! I’m working on the sorting step right now.
One thing I’m not clear on is how to expand the ranges from one step to the
next. The way GenomicInteractions are structured, there is a Granges object
with all possible ranges, and the GInteractions object is populated b
Hi Luke,
I also don’t see the visual representation. It sounds like you want to
summarise over disjoint boxes in the interaction heat map. It also sounds like
your strategy is to use quad-trees, truncated at a certain depth with all the
children accumulated to that depth. If so then what happen
Note that your visual won't show up for many (all?) of us. Nonetheless,
I think I know what you want to do.
Your task does not lend itself to vectorization, which makes it
difficult to write efficient R code. It's not impossible, but it would
be quite hard to read and debug, and your maintenance p
