Hi Martin, 

On Oct 7, 2010, at 7:44 PM, Martin Morgan wrote:
> 
> library(ShortRead)
> fl <- system.file("extdata", "ex1.bam", package="Rsamtools")
> fls <- c(fl, fl, fl)
> 
> qa <- do.call(rbind, Map(function(fl, id, ...) {
>    aln <- readAligned(fl, type="BAM", ...)
>    qa(aln, id)
> }, fls, paste(basename(fls), seq_along(fls), sep="-")))
> 

I'm not familiar with R errors but what about this? 

Error: Input/Output
  'readAligned' failed to parse files
  dirPath: './100927_s_1.bam'
  pattern: ''
  type: 'BAM'
  error: INTEGER() can only be applied to a 'integer', not a 'special'

Also, note that I've loaded files like this:

fls <- list.files(".", pattern="100927_", full.names=TRUE)

d

/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
e-mail: davide.cittaro@ifom-ieo-campus.it
*/




	[[alternative HTML version deleted]]

