[Bioc-devel] makeFeatureDbFromUCSC Column Checking

repeatDB <- makeFeatureDbFromUCSC("hg18", "RepeatMasker", "rmsk")
Download the rmsk table ... OK    # Takes a few minutes
Checking that required Columns are present ... 
Error in makeFeatureDbFromUCSC("hg18", "RepeatMasker", "rmsk") : 
  GenomicFeatures internal error: rmsk table doesn't contain a 'chrom', 'chromStart', or 'chromEnd' column and no reasonable substitute has been designated via the 'chromCol''chromStartCol' or 'chromEndCol' arguments.

---- Original message ----
Date: Tue, 15 May 2012 22:21:56 -0700
From: Herv? Pag?s <hpages at fhcrc.org>  
Subject: Re: [Bioc-devel] makeFeatureDbFromUCSC Column Checking  
To: ttriche at usc.edu
Cc: "Tim Triche, Jr." <tim.triche at gmail.com>, D.Strbenac at garvan.org.au, bioc-devel at r-project.org

Hi Dario, Tim,

Can you guys show an example so we know exactly what you mean. Sorry if
it's obvious. Thanks!

H.

On 05/15/2012 10:12 PM, Tim Triche, Jr. wrote:
seconding this!

On Tue, May 15, 2012 at 10:00 PM, Dario Strbenac
<D.Strbenac at garvan.org.au>wrote:

Hello,

I thought I'd suggest reordering the steps that are taken when
makeFeatureDbFromUCSC is called. It would be better if the column name
checking step was done before an entire table of data was downloaded and
then an error was thrown.

--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319
repeatDB<- makeFeatureDbFromUCSC("hg18", "RepeatMasker", "rmsk")
Download the rmsk table ... OK    # Takes a few minutes
Checking that required Columns are present ...
Error in makeFeatureDbFromUCSC("hg18", "RepeatMasker", "rmsk") :
   GenomicFeatures internal error: rmsk table doesn't contain a 'chrom', 'chromStart', or 'chromEnd' column and no reasonable substitute has been designated via the 'chromCol''chromStartCol' or 'chromEndCol' arguments.
Yes it was obvious (if I had read "makeFeatureDbFromUCSC" instead of
"makeTranscriptDbFromUCSC"). Makes a lot of sense and should be an easy
change. Thanks!

H.
---- Original message ----
Date: Tue, 15 May 2012 22:21:56 -0700
From: Herv? Pag?s<hpages at fhcrc.org>
Subject: Re: [Bioc-devel] makeFeatureDbFromUCSC Column Checking
To: ttriche at usc.edu
Cc: "Tim Triche, Jr."<tim.triche at gmail.com>, D.Strbenac at garvan.org.au, bioc-devel at r-project.org

Hi Dario, Tim,

Can you guys show an example so we know exactly what you mean. Sorry if
it's obvious. Thanks!

H.

On 05/15/2012 10:12 PM, Tim Triche, Jr. wrote:
seconding this!

On Tue, May 15, 2012 at 10:00 PM, Dario Strbenac
<D.Strbenac at garvan.org.au>wrote:

Hello,

I thought I'd suggest reordering the steps that are taken when
makeFeatureDbFromUCSC is called. It would be better if the column name
checking step was done before an entire table of data was downloaded and
then an error was thrown.

--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia

_______________________________________________
Bioc-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

--
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319