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
>
--
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274
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