[BioC] error in report(qa) from pkg ShortRead

[Martin Morgan]

On 09/11/2014 08:38 AM, Timothée Flutre wrote:
> Hello,
>
> I have a fastq file compressed with gzip in a directory named test/.
> I would like to assess its quality. Here is what I do:
>
> $ R
>> library(ShortRead)
>> qa <- qa("~/test", "fastq.gz")
>> report(qa, dest="~/test")
>
> And I get the following error message:
> Error in as.data.frame(lapply(df, sprintf, fmt = fmt)) :
> error in evaluating the argument 'x' in selecting a method for
> function 'as.data.frame': Error in FUN(X[[1L]], ...) :
> invalid format '%.3g'; use format %s for character objects
>
> Here are more details:
>> traceback()
> 7: as.data.frame(lapply(df, sprintf, fmt = fmt))
> 6: .df2a(qa[["adapterContamination"]])
> 5: hwrite(.df2a(qa[["adapterContamination"]]), border = 0)

I see you are in the half of the R users who dislike factors! I think

   qa[["adapterContamination"]]

should be a data.frame with a single column 'contamination', and that the single 
column should be a factor or numeric; I think you have set

   options(stringsAsFactors=FALSE)

and so instead of a factor or numeric it is character.

The workaround is to set options(stringsAsFactors=TRUE) (or not set this option 
at all!). This will be fixed in the next release of ShortRead.

Thanks for the report, and sorry for the inconvenience.

Martin

> 4: func(x, dest, type, ...)
> 3: func(x, dest, type, ...)
> 2: report(qa, dest = "~/test")
> 1: report(qa, dest = "~/test")
>
>> sessionInfo()
> R version 3.1.0 (2014-04-10)
> 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] ShortRead_1.22.0        GenomicAlignments_1.0.2 BSgenome_1.32.0
> [4] Rsamtools_1.16.1        GenomicRanges_1.16.3    GenomeInfoDb_1.0.2
> [7] Biostrings_2.32.1       XVector_0.4.0           IRanges_1.22.9
> [10] BiocParallel_0.6.1      BiocGenerics_0.10.0
>
> loaded via a namespace (and not attached):
> [1] BatchJobs_1.3       BBmisc_1.7          Biobase_2.24.0 [4]
> bitops_1.0-6        brew_1.0-6          checkmate_1.1 [7]
> codetools_0.2-8     compiler_3.1.0      DBI_0.2-7 [10] digest_0.6.4
>      fail_1.2            foreach_1.4.2 [13] grid_3.1.0
> hwriter_1.3.1       iterators_1.0.7 [16] lattice_0.20-29
> latticeExtra_0.6-26 RColorBrewer_1.0-5 [19] RSQLite_0.11.4
> sendmailR_1.1-2     stats4_3.1.0 [22] stringr_0.6.2       tools_3.1.0
>         zlibbioc_1.10.0
>
> Timothée Flutre
> Chargé de Recherche / Research Scientist
> INRA - Centre de Montpellier
>   http://umr-agap.cirad.fr/en
>   http://openwetware.org/wiki/User:Timothee_Flutre
>
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