[Bioc-devel] Rsamtools scanTabix Method Dispatch
On 12/15/2011 04:00 PM, Dario Strbenac wrote:
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 ?
Hi Dario -- Thanks for the bug report; look for version 1.6.3 for a fix. Use yieldTabix to get consecutive chunks of the file (including the whole thing in one big chunk). example(yieldTabix) res <- yieldTabix(TabixFile(fl)) Martin
-------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia
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