[BioC] error from rsamtools on 1000 genomes

[Martin Morgan]

On 07/02/2010 01:39 AM, Sergii Ivakhno wrote:
> Dear All,
> 
> I experience the following problem when trying to extract reads from bam
> files using Rsamtools on 1000 genomes hapmap BAM file. Would be grateful
> for your help, thanks.
> 
> Sergey
> 
>  
> 
>  
> 
> ########
> 
>  
> 
>  
> 
> w=GRanges(seqnames = "1",ranges = IRanges(1000,width=400))
> 
> p2 <- ScanBamParam(which=w)
> 
> res2 <- scanBam("NA12878.SLX.maq.SRP000031.2009_08.bam",p2)

Hi Sergii -- this should be

  res2 <- scanBam("NA12878.SLX.maq.SRP000031.2009_08.bam",param=p2)

i.e., provide the ScanBamParam as a named argument param=p2; see
?scanBam and example(scanBam) for some illustrations.

Also, Rsamtools only became available with R-2.11, so you've
mixed-and-matched R and Bioconductor versions; this will only result in
tears, so please update R and use biocLite() to install bioconductor
packages, as described at

  http://bioconductor.org/docs/install/

Martin


> 
>  
> 
>  
> 
> Error in as.character.default(x) :   no method for coercing this S4
> class to a vector
> 
>  
> 
>  
> 
>> sessionInfo()
> 
> R version 2.10.1 (2009-12-14)
> 
> x86_64-unknown-linux-gnu
> 
>  
> 
> locale:
> 
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
> 
>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
> 
>  [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8
> 
>  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
> 
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> 
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
> 
>  
> 
> attached base packages:
> 
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
>  
> 
> other attached packages:
> 
> [1] Rsamtools_1.0.5     Biostrings_2.16.6   GenomicRanges_1.0.4
> 
> [4] IRanges_1.6.8
> 
>  
> 
> loaded via a namespace (and not attached):
> 
> [1] Biobase_2.6.1
> 
>  
>   
> ----------------------------------------------
> Sergii Ivakhno
> 
> PhD student
> 
> Computational Biology Group
> Cancer Research UK Cambridge Research Institute
> Li Ka Shing Centre
> Robinson Way
> Cambridge CB2 0RE
> England
> 
> +44 (0)1223 404293 (O)
> +44 (0)1223 404128 (F)
> 
> http://www.compbio.group.cam.ac.uk <http://www.compbio.group.cam.ac.uk/>
> /
> 
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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