[Bioc-devel] makeFeatureDbFromUCSC Column Checking
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: 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
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-- 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