ject.org
> Subject: Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact =
> exact,
> upperBoundIsStrict = !allow.append) :
>
> Hi Thomas,
>
> On 10/25/2015 01:06 PM, Thomas Girke wrote:
> > I fixed this in systemPipeR versions 1.4.3/1.5.3. The reason for
a, Sonali
> <sar...@fredhutch.org>; bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact =
exact,
> upperBoundIsStrict = !allow.append) :
>
> Hi Thomas,
>
> On 10/25/2015 01:06 PM, Thomas Girke wrote:
> &g
> > Hervé Pagès
> > > Sent: Monday, October 26, 2015 12:39 PM
> > > To: Thomas Girke <thomas.gi...@ucr.edu>; Arora, Sonali
> > > <sar...@fredhutch.org>; bioc-devel@r-project.org
> > > Subject: Re: [Bioc-devel] system
Hi Thomas,
Thanks for the quick fix.
Sonali.
On 10/25/2015 1:06 PM, Thomas Girke wrote:
I fixed this in systemPipeR versions 1.4.3/1.5.3. The reason for this error
was that the tx_type column contains only NA values when a txdb is generated
with
makeTxDbFromUCSC(). Returning here something
Hi Thomas,
On 10/25/2015 01:06 PM, Thomas Girke wrote:
I fixed this in systemPipeR versions 1.4.3/1.5.3. The reason for this error
was that the tx_type column contains only NA values when a txdb is generated
with
makeTxDbFromUCSC(). Returning here something more meaningful may be useful,
such
Hi Hervé and Sonali,
Thanks for looking into this option. Your suggestion makes a lot of sense.
In general, I find it very useful to know what types of transcripts/genes
are included (or missing) in GRanges/GRangesList instances obtained from
txdb objects. For this, the tx_type classification is
I fixed this in systemPipeR versions 1.4.3/1.5.3. The reason for this error
was that the tx_type column contains only NA values when a txdb is generated
with
makeTxDbFromUCSC(). Returning here something more meaningful may be useful,
such as the transcript type information available when a txdb
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
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