[BioC] ShortReadQ and conversion of quality scores to characters

[Ivan Gregoretti]

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
>>
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>>
>
>
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