nice. I will play around with this. thanks Gabe!
On Fri, Dec 5, 2014 at 6:37 PM, Gabe Becker wrote:
> Hey guys,
>
> Surgically removed from promptClass:
>
> classInSig <- function(g, where, cl) {
> cl %in% unique(unlist(findMethods(g, where)@signatures))
> }
> genWithClass <- fu
Hey guys,
Surgically removed from promptClass:
classInSig <- function(g, where, cl) {
cl %in% unique(unlist(findMethods(g, where)@signatures))
}
genWithClass <- function(cl, where) {
allgen <- getGenerics(where = where)
ok <- as.logical(unlist(lapply(allgen, clas
Thanks, Herve. These are amazing improvements, and it's great to see that
the Ranges infrastructure continues to evolve and improve.
Michael
On Fri, Dec 5, 2014 at 1:17 PM, Hervé Pagès wrote:
> Developers,
>
> In BioC 3.1 the code behind overlap operations like findOverlaps(),
> countOverlaps()
Developers,
In BioC 3.1 the code behind overlap operations like findOverlaps(),
countOverlaps(), subsetByOverlaps(), summarizeOverlaps(), nearest(),
etc... has been refactored and improved. Some highlights on what has
changed:
- The underlying code used for finding/counting overlaps is now based
I believe that this question is better suited for the support site:
https://support.bioconductor.org/
On Thu, Dec 4, 2014 at 2:13 PM, Ian Misner wrote:
> Hello,
>
> I’m working with cummeRbund in R 3.1.1 and I’m trying to get a different
> point size for my csVolcano plot. I’ve tried two approac
Sounds good. One note: if range information becomes optional, it would be
nice if we could mark the availability of the information in the class
hierarchy. Otherwise, it's not easy to enforce a contract (that we can call
range-based methods on a SE) through dispatch. An alternative would be to
drop
Cool. I see hypertext as being useful here, because the generics and
classes form an intricate and sometimes ambiguous web, especially when
multiple inheritance and dispatch are involved. I think we should first
build better tooling for introspecting S4 and for graph-based modeling and
analysis of
On Thu, Dec 4, 2014 at 4:01 PM, Michael Lawrence
wrote:
>
> I think this gets at the heart of at least one of the usability issues in
> Bioconductor: interface discoverability. Many simpler command line tools have
> a single-faceted interface for which it is easy to enumerate a list of
> featur
Thanks Vince,
But actually I was planning to take this straight to the manual pages.
It's going to make for a longer manual page, but someone might find it
helpful down the line.
Marc
On 12/05/2014 10:14 AM, Marc Carlson wrote:
Hi Jelle,
Thank you for your patience in waiting for my an
Hi Jelle,
Thank you for your patience in waiting for my answer here. It took me a
lot longer to properly test and validate this than I initially expected.
So if you look at amigo you can see these graph views that show you what
the current terms up and downstream of a given GO term should be
How exactly do we "tune in" to this hangout? Is there some sort of URL?
On Tue, Dec 2, 2014 at 3:08 PM, Marc Carlson wrote:
> Hello new package authors,
>
> Based on the number of new software packages being submitted to the
> project it seems that Bioconductor is more popular than ever. Last r
The two data structures do not encode the same information. Coercion to VCF
forms a rectangular matrix: position+alt by sample. There is no standard
way to encode that a given cell in that matrix is absent, so coercion to
VRanges simply maps each cell to an element. One could imagine using the
"."
Hi,
I am trying to build a genome which is not listed in BSgenome but
unfortunately getting following error at *R CMD check * level:
* installing *source* package ‘BSgenome.Ntabacum.SOLG.K326’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building p
Hi,
Assume that we have two variants from two samples at the same locus,
stored in a 'VRanges' or 'VCF' object:
library(VariantAnnotation)
vr = VRanges("1", IRanges(c(10, 10), width = 1),
ref = c("C", "C"), alt = c("A", "G"),
sampleNames = c("S1", "S2"))
vcf = as(vr, "VCF")
If we
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