Error using the id function of ShortReadQ object
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Guest User ★ 12k
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Last seen 8.1 years ago
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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Bernd Klaus ▴ 600
@bernd-klaus-6281
Last seen 4.0 years ago
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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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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