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Tim Rayner
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270
@tim-rayner-2913
Last seen 10.2 years ago
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