On 1/30/20 13:17, Michael Lawrence wrote:
> That sucks. It was broken since it was added in 2017... now fixed.
Unfortunately these things tend to happen to stuff that doesn't have
examples or unit tests.
Thanks for the fix!
H.
___
That sucks. It was broken since it was added in 2017... now fixed.
On Thu, Jan 30, 2020 at 11:20 AM Pages, Herve wrote:
>
> On 1/30/20 11:10, Hervé Pagès wrote:
> > Yes poverlaps() is a good option, as mentioned earlier.
>
> Well actually not. Looks like it's broken:
>
> >
On 1/30/20 11:10, Hervé Pagès wrote:
> Yes poverlaps() is a good option, as mentioned earlier.
Well actually not. Looks like it's broken:
> poverlaps(GRanges("chr1:11-15"), GRanges("chr1:16-20"))
Error in isSingleNumber(minoverlap) : object 'minoverlaps' not found
H.
Yes poverlaps() is a good option, as mentioned earlier. I was just
commenting about doing something like:
out <- vector("numeric", length(x))
out[(which(foo(x))] <- 1
when you can just do:
out <- foo(x)
H.
On 1/30/20 10:56, Michael Lawrence wrote:
> What happened to just
What happened to just poverlaps()?
On Thu, Jan 30, 2020 at 10:34 AM Pages, Herve wrote:
>
> On 1/29/20 23:31, web working wrote:
> > Hi Herve,
> >
> > Thank you for your answer. pcompare works fine for me. Here my solution:
> >
> > query <- GRanges(rep("chr1", 4), IRanges(c(1, 5, 9, 20), c(2, 6,
On 1/29/20 23:31, web working wrote:
> Hi Herve,
>
> Thank you for your answer. pcompare works fine for me. Here my solution:
>
> query <- GRanges(rep("chr1", 4), IRanges(c(1, 5, 9, 20), c(2, 6, 10, 22)))
> subject <- GRanges(rep("chr1",4), IRanges(c(3, 1, 1, 15), c(4, 2, 2, 21)))
> out <-
Hi Herve,
Thank you for your answer. pcompare works fine for me. Here my solution:
query <- GRanges(rep("chr1", 4), IRanges(c(1, 5, 9, 20), c(2, 6, 10, 22)))
subject <- GRanges(rep("chr1",4), IRanges(c(3, 1, 1, 15), c(4, 2, 2, 21)))
out <- vector("numeric", length(query))
On 1/29/20 13:14, Jianhong Ou, Ph.D. wrote:
> Oh, I forget that. Thank you for reminder.
> Then how about:
>
> distance(query, narrow(subject, start=2, end=-2)) == 0
>
> ?
Yep, that's more accurate. With the following gotcha:
'narrow(subject, start=2, end=-2)' will fail if 'subject'
Oh, I forget that. Thank you for reminder.
Then how about:
distance(query, narrow(subject, start=2, end=-2)) == 0
?
On 1/29/20, 12:40 PM, "Pages, Herve" wrote:
On 1/29/20 08:04, Jianhong Ou, Ph.D. wrote:
> Try
> dist=distance(query, subject)
> dist==0
> ?
On 1/29/20 08:04, Jianhong Ou, Ph.D. wrote:
> Try
> dist=distance(query, subject)
> dist==0
> ?
Please be aware that dist==0 does NOT mean that 2 ranges overlap. It
means that they overlap OR are **adjacent**:
> distance(GRanges("chr1:1-20"), GRanges("chr1:21-25"))
[1] 0
H.
>
> On 1/29/20,
Yes poverlaps().
Or pcompare(), which should be even faster. But only if you are not
afraid to go low-level. See ?rangeComparisonCodeToLetter for the meaning
of the codes returned by pcompare().
H.
On 1/29/20 08:01, Michael Lawrence via Bioc-devel wrote:
> poverlaps()?
>
> On Wed, Jan 29,
Try
dist=distance(query, subject)
dist==0
?
On 1/29/20, 10:50 AM, "Bioc-devel on behalf of web working"
wrote:
Hello,
I have two big GRanges objects and want to search for an overlap of the
first range of query with the first range of subject. Then take the
second
poverlaps()?
On Wed, Jan 29, 2020 at 7:50 AM web working wrote:
>
> Hello,
>
> I have two big GRanges objects and want to search for an overlap of the
> first range of query with the first range of subject. Then take the
> second range of query and compare it with the second range of subject
>
Hello,
I have two big GRanges objects and want to search for an overlap of the
first range of query with the first range of subject. Then take the
second range of query and compare it with the second range of subject
and so on. Here an example of my problem:
# GRanges objects
query <-
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