[BioC] ShortRead with BAM

[James W. MacDonald]

Hi Duke,

Still the wrong list. You want Bioc-sig-sequencing.

Duke wrote:
> Hi all,
> 
> I am totally new to both R and BioConductor, so please be easy on me. I 
> just updated my R package to 2.11, and installed new ShortRead package, 
> but it seems that I am doing something wrong, and that there is some 
> changes from ShortRead 1.5 to 1.6 (like the command format etc...). I 
> tried to read a BAM file by creating a file as follow:

You don't want the ShortRead package. You want Rsamtools, and the 
scanBam() function. See ?scanBam for more info.

Best,

Jim


> 
> library(ShortRead)
> sp <- SolexaPath('/Volumes/Data/analysis/glamblia/STATs')
> ap <- analysisPath(sp)
> (aln0 <- readAligned(ap, "WB4day.bwa.def.bam", "BAM"))
> 
> but running the above just gave me the content of dirPath function. My 
> package infos is:
> 
>  > sessionInfo()
> R version 2.11.0 (2010-04-22)
> x86_64-apple-darwin9.8.0
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] ShortRead_1.6.0     Rsamtools_1.0.0     lattice_0.18-5
> [4] Biostrings_2.16.0   GenomicRanges_1.0.1 IRanges_1.6.0
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0 grid_2.11.0   hwriter_1.2   tools_2.11.0
> 
> Anybody has any idea?
> 
> Thanks,
> 
> D.
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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