[BioC] Error using the id function of ShortReadQ object

[Tomas Bjorklund [guest]]

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.