Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

2015-12-01 Thread Cook, Malcolm
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

Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

2015-12-01 Thread Hervé Pagès
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

Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

2015-12-01 Thread Thomas Girke
> > 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

Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

2015-10-26 Thread Arora, Sonali
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

Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

2015-10-26 Thread Hervé Pagès
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

Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

2015-10-26 Thread Thomas Girke
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

Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

2015-10-25 Thread Thomas Girke
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

Re: [Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

2015-10-22 Thread Thomas Girke
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

[Bioc-devel] systemPipeR error - Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :

2015-10-22 Thread Arora, Sonali
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