The code that's there now is already unit tested and should be merged.
The test I mentioned was a small check that the following works (this is
what started this thread):
> m <- matrix(1, 5, 3, dimnames=list(NULL, NULL))
> gr <- GRanges("chr1", IRanges(1:5, 10))
> colData <- DataFrame(x=letters[1:
If you don't mind, I think I'll wait till after you're finished testing
before merging.
Please keep me up to date,
Michael
On Fri, Aug 2, 2013 at 7:43 AM, Hector Corrada Bravo wrote:
> Thanks again Kasper,
> All of these are now fixed:
> * empty subject seqlevel,
> * out-of-order seqinfo's,
> *
Thanks again Kasper,
All of these are now fixed:
* empty subject seqlevel,
* out-of-order seqinfo's,
* show,GIntervalTree-method
Michael, please merge from
https://github.com/hcorrada/IRanges [version 1.19.20]
https://github.com/hcorrada/GenomicRanges [version 1.13.36]
I'll test the SummarizedExp
If you're fixing tonight here is a possible related. I get an error when I
do the findOverlaps and I have two GRanges with the same seqlevels but in
different order (so, I guess, technically not the same seqlevels). If this
is not supported, I suggest an upfront check.
gr1 = GRanges(seqnames = c
Minor thing: the show method for GIntervalTrees is saying 'A GRanges with
...'. Perhaps this should be changed to 'A GIntervalTree with ...'
Kasper
On Thu, Aug 1, 2013 at 4:48 PM, Hector Corrada Bravo wrote:
> Thanks. I'll fix tonight.
>
>
> On Thu, Aug 1, 2013 at 4:28 PM, Kasper Daniel Hanse
Thanks. I'll fix tonight.
On Thu, Aug 1, 2013 at 4:28 PM, Kasper Daniel Hansen
wrote:
> Bug:
>> library(GenomicRanges) ## 1.13.35
>> gr = GRanges(seqnames = c("chr1", "chr2"), ranges = IRanges(1:2, width =
> 1))
> > gr.tree <- GIntervalTree(gr)
> > findOverlaps(gr.tree, gr.tree)
> Hits of len
Bug:
> library(GenomicRanges) ## 1.13.35
> gr = GRanges(seqnames = c("chr1", "chr2"), ranges = IRanges(1:2, width =
1))
> gr.tree <- GIntervalTree(gr)
> findOverlaps(gr.tree, gr.tree)
Hits of length 2
queryLength: 2
subjectLength: 2
queryHits subjectHits
1
Ah! Super-nice! I'll test as well, when I have time.
Kasper
On Thu, Aug 1, 2013 at 3:34 PM, Hector Corrada Bravo wrote:
> This is not tested, but...
>
> GIntervalTree extends GenomicRanges so, in principle, can be used in the
> rowData slot of SummarizedExperiment. I tried to make GIntervalTr
This is not tested, but...
GIntervalTree extends GenomicRanges  so, in principle, can be used in the
rowData slot of SummarizedExperiment. I tried to make GIntervalTree support as
much of the GenomicRanges interface as I could so this may work already for
overlap queries where the SummarizedE
Now that we have GIntervalTree, I am really interested in a
SummarizedExperiment that stores its index in a slot, so it can be indexed
once. I am sure other people are greedily eyeing this as well. Either
changing the class or extending it.
Unfortunately, I will not have time to work on this for
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