[Bioc-devel] Rsamtools scanTabix Method Dispatch

[Dario Strbenac]

Hello,

This looks like a bug.

library(Rsamtools)

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
Australia