Hi Tim,

Good catch. Added a test to catch that in the future. Fixed in 1.16.3 (and
devel).

Michael

On Mon, Jul 16, 2012 at 6:25 AM, Tim Rayner <tfrayner@gmail.com> wrote:

> Hi,
>
> I've just run into what I think is a bug in the rtracklayer
> import.gff3 function (v1.16.1). If I import a GFF3 containing scores
> while stringsAsFactors=TRUE, the resulting scores are mangled. I
> haven't confirmed it, but I suspect the values are being converted to
> a factor upon import and then coerced to numeric (giving the factor
> level, not the original value). If I use
> options(stringsAsFactors=FALSE) the values remain intact.
>
> Best regards,
>
> Tim Rayner
>
> --
> Bioinformatician
> Smith Lab, CIMR
> University of Cambridge
> United Kingdom
>
>
>
> Example GFF3 content:
>
> ##gff-version 3
> ##date 2012-07-13
> chr1    rtracklayer     snp        189807684       189807684
> 0.20294398632582        *       .       ID=rs955894;name=rs955894
> chr1    rtracklayer     snp        198484784       198484784
> 0.269327708380075       *       .       ID=rs16843226;name=rs16843226
> chr1    rtracklayer     snp        237405093       237405093
> 0.379417274542624       *       .       ID=rs679735;name=rs679735
> chr1    rtracklayer     snp        80235819        80235819
> 0.418346673826376       *       .       ID=rs12022561;name=rs12022561
> chr1    rtracklayer     snp        84875173        84875173
> 0.302119655250906       *       .       ID=rs6576700;name=rs6576700
> chr1    rtracklayer     snp        112793146       112793146
> 0.390270490589027       *       .       ID=rs11102440;name=rs11102440
> chr1    rtracklayer     snp        244187847       244187847
> 0.249206080122631       *       .       ID=rs1000451;name=rs1000451
> chr1    rtracklayer     snp        8612104 8612104 0.583436890885292
>     *       .       ID=rs6577499;name=rs6577499
>
>
> > sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rtracklayer_1.16.1  GenomicRanges_1.8.6 IRanges_1.14.3
> [4] BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.24.1 bitops_1.0-4.1    BSgenome_1.24.0   RCurl_1.91-1
> [5] Rsamtools_1.8.5   stats4_2.15.1     tools_2.15.1      XML_3.9-4
> [9] zlibbioc_1.2.0
>
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