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,
Just after I pressed the "Send" button I realized that by returning a
new SE object you probably meant returning an SE object with only the
new assay in it. I would favor the other option i.e. 'doProcess(se)'
adds a new assay to 'se'. I think that's what most workflows based on SE
objects do.
On 1/28/20 01:37, Laurent Gatto wrote:
> Dear all,
>
> Assume we have a SummarizedExperiment object `se` that contains raw count
> data, and a method `doProcess` that processes the data to produce a matrix of
> identical dimensions (for example log-transformation, normalisation,
> imputation,
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 <-
Hi,
I've activated your account from my end and set a temp password.
I'll send you a private email with the temp password. Please make sure to
change your password after that.
Best,
Nitesh
> On Jan 28, 2020, at 1:43 PM, Danrley Fernandes wrote:
>
> Hi,
> I'm the developer of the package
Hi
I've just activated the account for you and set a temp password. I'll send that
to you privately.
You should then be able to access your account, add SSH keys if needed and then
access your package.
Nitesh
> On Jan 29, 2020, at 9:41 AM, Richard Virgen-Slane
> wrote:
>
> Hi All,
>
>
Hi All,
I tried to activate rvs.bioto...@gmail.com and I got: rvs.bioto...@gmail.com is
not associated with a maintainer of a Bioconductor package. Please check
the spelling or contact bioc-devel@r-project.orgfor help.
I still can’t activate my account even though I copied at pasted my email
Should be pushed now.
Best,
Tim
Am Mi., 29. Jan. 2020 um 14:47 Uhr schrieb Shepherd, Lori <
lori.sheph...@roswellpark.org>:
> Have you been able to access your account? I still do not see any pushes
> to the git.bioconductor.org repository to fix your broken package?
>
> Lori Shepherd
>
>
Have you been able to access your account? I still do not see any pushes to
the git.bioconductor.org repository to fix your broken package?
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Many reported an issue with the vignettes building when using BiocStyle
https://github.com/Bioconductor/BiocStyle/issues/71
We traced it back to an issue with knitr.
https://github.com/yihui/knitr/issues/1797
While knitr fixed the issue, it has not been pushed officially to CRAN as of
yet so
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