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

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]