Hi Tengfei,
Yes that looks like an oversight. Thanks for reporting that! I will
extend makeTxDbPackage so that it's more accommodating of these newer
transcriptDbs. If you want to help me out, you could call saveDb() on
your gmax189 object and send me the .sqlite file that you save it to.
Also, if you have any alternate options for importing your data (other
than using GFF or GTF): I think you probably should consider it. The
file specifications for these filetypes are missing key details and so
you can very easily get a "legal" GFF or GTF file that is actually
missing important details from it's contents. For example, they can
commonly lack information about the order of the exons for a given
transcript, which can render them difficult (or impossible) to use for
transcript work. But for these specifications, that information is
"optional".
Marc
On 02/06/2013 09:46 PM, Tengfei Yin wrote:
Dear all,
I am trying to build a txdb object from gff3 for soybean data and try to
make it a package. Code used like this
gmax189<- makeTranscriptDbFromGFF("~/Gmax_189_gene_exons.gff3",
format = "gff3", species = "Glycine max",
dataSource = "http://www.phytozome.org/";)
makeTxDbPackage(txdb = gmax189,
version = "0.9.1",
maintainer = "Tengfei Yin",
author = "Tengfei Yin",
destDir=".",
license="Artistic-2.0")
Error message:
Error in gsub("_", "", pkgName) :
error in evaluating the argument 'x' in selecting a method for function
'gsub': Error: object 'pkgName' not found
Looks like my dataSource should be either BioMart or UCSC, otherwise no
pkgname will be produced in function .makePackageName?
Or should I build annotation package in some other ways?
Thanks a lot
Tengfei
my sessionInfo
sessionInfo()
R Under development (unstable) (2013-01-21 r61728)
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=C 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] GenomicFeatures_1.11.8 AnnotationDbi_1.21.10 Biobase_2.19.2
[4] GenomicRanges_1.11.28 IRanges_1.17.31 BiocGenerics_0.5.6
loaded via a namespace (and not attached):
[1] biomaRt_2.15.0 Biostrings_2.27.10 bitops_1.0-5
BSgenome_1.27.1
[5] DBI_0.2-5 RCurl_1.95-3 Rsamtools_1.11.15
RSQLite_0.11.2
[9] rtracklayer_1.19.9 stats4_3.0.0 tools_3.0.0 XML_3.95-0.1
[13] zlibbioc_1.5.0
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