[BioC] Devel version of easyRNASeq: using the simpleRNASeq method gives an error

Sylvain Foisy Ph. D. sylvain.foisy at diploide.net
Thu Mar 27 14:40:36 CET 2014

Hi to all,

I am trying to use the R-devel branch for easyRNASeq to get gene counts from filtered BAM files and I get the following error:

> exp<-simpleRNASeq(bamFiles = bfl, param = rParam, nnodes = 1, verbose = TRUE)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘simpleRNASeq’ for signature ‘"BamFileList”’

According to the help material, simpleRNASeq should need this:

     simpleRNASeq(bamFiles = BamFileList(),
       param = RnaSeqParam(), nnodes = 1, verbose = FALSE)

When I check the nature of my bfl object, I get this:

> bfl
BamFileList of length 103
names(103): 123456_CELLTYPE_B_accepted_hits_properly_paired.bam …

So bfl is the right type… Any ideas or is this a bug? It’s the devel version after all ;-)

Best regards


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