They're enclosed in different environments, for one. Basically, all bets
are off if you're doing the unload, reinstall library cycle.
On Thu, Oct 22, 2015 at 7:00 PM, Dario Strbenac
wrote:
> Good day,
>
> The variables have the same contents.
>
> Browse[1]> selectParams@featureSelection
> nonsta
Good day,
The variables have the same contents.
Browse[1]> selectParams@featureSelection
nonstandardGenericFunction for "DMDselection" defined from package "ClassifyR"
function (expression, ...)
{
standardGeneric("DMDselection")
}
Methods may be defined for arguments: expression
Use showM
Is getGeneric("DMDselection") identical to your
selectParams@featureSelection? You'll want to get rid of the { } in your
generic definition in order to avoid the non-standard generic.
On Thu, Oct 22, 2015 at 6:00 PM, Dario Strbenac
wrote:
> Hello,
>
> How is it possible to have the method imple
Hello,
How is it possible to have the method implemented for a particular signature,
but not found ? The problem I am having is :
Browse[2]> showMethods("DMDselection")
Function: DMDselection (package ClassifyR)
expression="ExpressionSet"
expression="matrix"
Browse[2]> selectParams@featureSelect
Thanks. Good to know. I have never tried this with an txdb instance from
makeTxDbFromUCSC(). Will fix this over the weekend.
Thomas
On Thu, Oct 22, 2015 at 5:39 PM Arora, Sonali wrote:
> Hi Thomas,
>
> I get the following error when I try to obtain the feature types using
> the function genFeatu
Hi Thomas,
I get the following error when I try to obtain the feature types using
the function genFeatures()
> library(systemPipeR)
> library(GenomicFeatures)
Loading required package: AnnotationDbi
> txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene")
Download the refGene table
Hi Thomas,
Thanks for tagging your package with RiboSeq - Sorry about missing
systemPipeR in my last email.
Sonali.
On 10/20/2015 4:34 PM, Arora, Sonali wrote:
Recently a new biocView called 'RiboSeq' was added to the list of
biocViews to tag packages working with Ribsome Profiling Sequenc
Hi Aaron, Dan,
thank you for reporting this! When I suggested adding the TOC I didn't
realize that the md_document() doesn't output it hyperlinked - my fault!
I was also surprised to find out that there is no easy fix for it as there
is no option for this in pandoc/rmarkdown.
However, I already
- Original Message -
> From: "Aaron Lun"
> To: "Dan Tenenbaum"
> Cc: "bioc-devel"
> Sent: Thursday, October 22, 2015 8:45:58 AM
> Subject: Re: [Bioc-devel] Bioconductor Workflows: TOC and displaying document
> details
> Hi Dan,
>
> The added TOC looks good; but can the lines also be
Hi Dan,
The added TOC looks good; but can the lines also be hyperlinked to the
appropriate (sub)sections? This would make it a lot easier to use, like:
https://www.bioconductor.org/help/workflows/variants
Right now, it's like I'm reading a physical book; I'm pressing the TOC
line with my fin
Just for the record, I've removed the usage of ifelse() by VRanges in
release and devel.
On Wed, Oct 21, 2015 at 6:50 AM, Robert Castelo
wrote:
> hi,
>
> one of the recent changes in the devel IRanges has been to defunct the
> 'ifelse' method for 'Rle' objects. This was warned during the previou
Michael, Hervé,
thanks for your enlightening discussion about proper overload of base::
methods. I guess you're going to take action on the S4Vectors package
(and not IRanges, as I wrongly put on the subject), right?
i'm afraid i lack a full understanding of what are the best practices
when
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