[Bioc-devel] makeFeatureDbFromUCSC Column Checking

Hervé Pagès hpages at fhcrc.org
Wed May 16 18:24:21 CEST 2012


On 05/15/2012 11:00 PM, Dario Strbenac wrote:
>> 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: 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


-- 
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



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