[BioC] Error using the id function of ShortReadQ object

[Bernd Klaus]

Hi Thomas,

the id function from the  plyr package hides the id function from the ShortRead package,
this is where the strange error comes from.

If you want to use the id function from ShortRead explicitly, just type
ShortRead::id(FastQ1)

This can be useful whenever you experience a very strange error message,
 for example the qvalue package has a function 
qplot that hides the one from ggplot2 ...


Best wishes,

Bernd


On May 18, 2014, at 11:58 AM, Tomas Bjorklund [guest] <guest at bioconductor.org> wrote:

> I have a strange issue when trying to extract the id from a ShortReadQ object generated from Pacific Bioscience RSII FASTQ files. 
> 
> Here are the commands I ran:
> 
>> FastQ1 <- readFastq(FastQFile1)
>> id(FastQ1)
> Error in as.list.default(X) : 
>  no method for coercing this S4 class to a vector
>> FastQ1 at id
>  A BStringSet instance of length 82156
>        width seq
>    [1]    64 m131010_133936_42203_c100579852550000001823088204021445_s1_p0/31
>    [2]    64 m131010_133936_42203_c100579852550000001823088204021445_s1_p0/53
>    [3]    64 m131010_133936_42203_c100579852550000001823088204021445_s1_p0/57
>    [4]    64 m131010_133936_42203_c100579852550000001823088204021445_s1_p0/61
>    [5]    64 m131010_133936_42203_c100579852550000001823088204021445_s1_p0/67
>    ...   ... ...
> [82152]    67 m131010_181229_42203_c100579852550000001823088204021447_s1_p0/58163
> [82153]    67 m131010_112316_42203_c100579852550000001823088204021444_s1_p0/97541
> [82154]    67 m131010_155556_42203_c100579852550000001823088204021446_s1_p0/73177
> [82155]    68 m131010_181229_42203_c100579852550000001823088204021447_s1_p0/109202
> [82156]    68 m131010_181229_42203_c100579852550000001823088204021447_s1_p0/113290
> 
> 
> How come that the "Private" @id works but not the recommended id() ?
> 
> Thank you for all the excellent help on this maininglist!
> 
> /Tomas
> 
> 
> 
> -- output of sessionInfo(): 
> 
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] foreach_1.4.2           ggplot2_0.9.3.1         plyr_1.8.1              ShortRead_1.22.0        GenomicAlignments_1.0.1 BSgenome_1.32.0        
> [7] Rsamtools_1.16.0        GenomicRanges_1.16.3    GenomeInfoDb_1.0.2      Biostrings_2.32.0       XVector_0.4.0           IRanges_1.22.6         
> [13] BiocParallel_0.6.0      BiocGenerics_0.10.0    
> 
> loaded via a namespace (and not attached):
> [1] BatchJobs_1.2       BBmisc_1.6          Biobase_2.24.0      bitops_1.0-6        brew_1.0-6          codetools_0.2-8     colorspace_1.2-4   
> [8] DBI_0.2-7           digest_0.6.4        fail_1.2            grid_3.1.0          gtable_0.1.2        hwriter_1.3         iterators_1.0.7    
> [15] labeling_0.2        lattice_0.20-29     latticeExtra_0.6-26 MASS_7.3-31         munsell_0.4.2       proto_0.3-10        RColorBrewer_1.0-5 
> [22] Rcpp_0.11.1         reshape2_1.4        RSQLite_0.11.4      scales_0.2.4        sendmailR_1.1-2     stats4_3.1.0        stringr_0.6.2      
> [29] tools_3.1.0         zlibbioc_1.10.0    
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
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