[Bioc-devel] Rsamtools scanTabix Method Dispatch

Dario Strbenac D.Strbenac at garvan.org.au
Fri Dec 16 01:00:11 CET 2011


This looks like a bug.


gr <- GRanges("chr1", IRanges(1, 999999999))
txs <- scanTabix("http://savantbrowser.com/data/hg18/hg18.refGene.gz", param = gr)

Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "scanTabix", for signature "TabixFile", "missing"

I have Rsamtools_1.6.2 in R version 2.14.0 (2011-10-31)

One more related question. Is it possible to get all records from a tabix file without looping over each chromosome and collapsing the list at the end ?

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

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