ShortReadQ and conversion of quality scores to characters
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@ivan-gregoretti-3975
Last seen 6.6 years ago
Canada
Hello everyone, Could somebody show how to convert ShortReadQ qualities to characters? A little detail: For instance, I can load into memory a ShortReadQ instance, A <- readFastq('file.fq.gz') and then I can convert to character either the ID lines or the sequences, as.character(id(A)) as.character(sread(A)) For qualities however, the analogous operation cannot be performed, > as.character(quality(A) Error in as.character.default(quality(A)) : no method for coercing this S4 class to a vector That is very unfortunate. Could somebody enlighten me? Thank you, Ivan Ivan Gregoretti, PhD Bioinformatics > sessionInfo() R Under development (unstable) (2014-06-29 r66051) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] lattice_0.20-29 sqldf_0.4-7.1 RSQLite.extfuns_0.0.1 [4] RSQLite_0.11.4 DBI_0.2-7 gsubfn_0.6-5 [7] proto_0.3-10 stringr_0.6.2 ShortRead_1.22.0 [10] GenomicAlignments_1.0.1 BSgenome_1.32.0 Rsamtools_1.16.1 [13] GenomicRanges_1.16.3 GenomeInfoDb_1.0.2 Biostrings_2.32.0 [16] XVector_0.4.0 IRanges_1.22.9 BiocParallel_0.6.1 [19] BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] BatchJobs_1.2 BBmisc_1.7 Biobase_2.24.0 [4] bitops_1.0-6 brew_1.0-6 checkmate_1.1 [7] chron_2.3-45 codetools_0.2-8 digest_0.6.4 [10] fail_1.2 foreach_1.4.2 grid_3.2.0 [13] hwriter_1.3 iterators_1.0.7 latticeExtra_0.6-26 [16] plyr_1.8.1 RColorBrewer_1.0-5 Rcpp_0.11.2 [19] sendmailR_1.1-2 stats4_3.2.0 tcltk_3.2.0 [22] tools_3.2.0 zlibbioc_1.10.0
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@martin-morgan-1513
Last seen 4 days ago
United States
On 07/11/2014 09:48 AM, Ivan Gregoretti wrote: > Hello everyone, > > Could somebody show how to convert ShortReadQ qualities to characters? > > > A little detail: > > For instance, I can load into memory a ShortReadQ instance, > > A <- readFastq('file.fq.gz') > > and then I can convert to character either the ID lines or the sequences, > > as.character(id(A)) > as.character(sread(A)) > > For qualities however, the analogous operation cannot be performed, > >> as.character(quality(A) > Error in as.character.default(quality(A)) : > no method for coercing this S4 class to a vector > > > That is very unfortunate. Could somebody enlighten me? as.character(quality(quality(A)) (the double quality() is because of how the class was designed). Martin > > Thank you, > > Ivan > > > Ivan Gregoretti, PhD > Bioinformatics > > >> sessionInfo() > R Under development (unstable) (2014-06-29 r66051) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] lattice_0.20-29 sqldf_0.4-7.1 RSQLite.extfuns_0.0.1 > [4] RSQLite_0.11.4 DBI_0.2-7 gsubfn_0.6-5 > [7] proto_0.3-10 stringr_0.6.2 ShortRead_1.22.0 > [10] GenomicAlignments_1.0.1 BSgenome_1.32.0 Rsamtools_1.16.1 > [13] GenomicRanges_1.16.3 GenomeInfoDb_1.0.2 Biostrings_2.32.0 > [16] XVector_0.4.0 IRanges_1.22.9 BiocParallel_0.6.1 > [19] BiocGenerics_0.10.0 > > loaded via a namespace (and not attached): > [1] BatchJobs_1.2 BBmisc_1.7 Biobase_2.24.0 > [4] bitops_1.0-6 brew_1.0-6 checkmate_1.1 > [7] chron_2.3-45 codetools_0.2-8 digest_0.6.4 > [10] fail_1.2 foreach_1.4.2 grid_3.2.0 > [13] hwriter_1.3 iterators_1.0.7 latticeExtra_0.6-26 > [16] plyr_1.8.1 RColorBrewer_1.0-5 Rcpp_0.11.2 > [19] sendmailR_1.1-2 stats4_3.2.0 tcltk_3.2.0 > [22] tools_3.2.0 zlibbioc_1.10.0 > > _______________________________________________ > 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 > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Thank you. Ivan On Fri, Jul 11, 2014 at 3:45 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > On 07/11/2014 09:48 AM, Ivan Gregoretti wrote: >> >> Hello everyone, >> >> Could somebody show how to convert ShortReadQ qualities to characters? >> >> >> A little detail: >> >> For instance, I can load into memory a ShortReadQ instance, >> >> A <- readFastq('file.fq.gz') >> >> and then I can convert to character either the ID lines or the sequences, >> >> as.character(id(A)) >> as.character(sread(A)) >> >> For qualities however, the analogous operation cannot be performed, >> >>> as.character(quality(A) >> >> Error in as.character.default(quality(A)) : >> no method for coercing this S4 class to a vector >> >> >> That is very unfortunate. Could somebody enlighten me? > > > as.character(quality(quality(A)) > > (the double quality() is because of how the class was designed). > > Martin > >> >> Thank you, >> >> Ivan >> >> >> Ivan Gregoretti, PhD >> Bioinformatics >> >> >>> sessionInfo() >> >> R Under development (unstable) (2014-06-29 r66051) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] lattice_0.20-29 sqldf_0.4-7.1 >> RSQLite.extfuns_0.0.1 >> [4] RSQLite_0.11.4 DBI_0.2-7 gsubfn_0.6-5 >> [7] proto_0.3-10 stringr_0.6.2 ShortRead_1.22.0 >> [10] GenomicAlignments_1.0.1 BSgenome_1.32.0 Rsamtools_1.16.1 >> [13] GenomicRanges_1.16.3 GenomeInfoDb_1.0.2 Biostrings_2.32.0 >> [16] XVector_0.4.0 IRanges_1.22.9 BiocParallel_0.6.1 >> [19] BiocGenerics_0.10.0 >> >> loaded via a namespace (and not attached): >> [1] BatchJobs_1.2 BBmisc_1.7 Biobase_2.24.0 >> [4] bitops_1.0-6 brew_1.0-6 checkmate_1.1 >> [7] chron_2.3-45 codetools_0.2-8 digest_0.6.4 >> [10] fail_1.2 foreach_1.4.2 grid_3.2.0 >> [13] hwriter_1.3 iterators_1.0.7 latticeExtra_0.6-26 >> [16] plyr_1.8.1 RColorBrewer_1.0-5 Rcpp_0.11.2 >> [19] sendmailR_1.1-2 stats4_3.2.0 tcltk_3.2.0 >> [22] tools_3.2.0 zlibbioc_1.10.0 >> >> _______________________________________________ >> 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 >> > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793
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