Breaker breaker.
1) A package to define a base (virtual) "Interactions" class. This would
basically have a constant "Vector" store with a "Hits" object specifying
the pairwise interactions between elements in the constant store. One
could also distinguish between "SelfInteractions" (constant s
Power's back, so continuing on:
The Bioconductor Hi-C infrastructure should probably be consolidated
into packages with more clearly defined boundaries:
1) A package to define a base (virtual) "Interactions" class. This would
basically have a constant "Vector" store with a "Hits" object speci
Hi Luke,
Do you mean bins or bin pairs?
If you want to just bin the coverage in terms of the linear genome,
there should be ways to do that outside of InteractionSet or
GenomicInteractions. This is just dealing with standard genomic interval
data; extract the anchor coordinates and plug it in
Maybe the question arises whether to store a reduced representation like, say,
singleCellExperiment does?
In any event, I agree that endomorphism will be expected by users and, like
tximport collapsing many transcripts into each gene, the sensible thing to do
is just to return a binned (less ro
Why is this not "just" a function which transforms one GI into another GI?
Thats what it seems to me.
On Fri, Mar 22, 2019 at 12:31 PM Luke Klein wrote:
> I am writing a package that will extend the GenomicInteractions class. I
> am a statistician, so I may not know best practices when it comes
I am writing a package that will extend the GenomicInteractions class. I am a
statistician, so I may not know best practices when it comes to extending
existing classes (eg. should I make a new slot or simply add a column to the
`elementMetadata`? Are there existing functions that already do w
