[Bioc-devel] makeFeatureDbFromUCSC Column Checking

[Dario Strbenac]

> 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: Hervé Pagès <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
>>>
>>
>>
>>
>
>
>-- 
>Hervé Pagès
>
>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