[BioC] ShortReadQ and conversion of quality scores to characters

Ivan Gregoretti ivangreg at gmail.com
Fri Jul 11 18:48:32 CEST 2014


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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