Entering edit mode
Hi,
I got error when I make transcript db from ucsc for mm8. Could anybody
help me to figure out this? Thanks in advance.
Error in tableNames(ucscTableQuery(session, track = track)) :
error in evaluating the argument 'object' in selecting a method for
function 'tableNames': Error in normArgTrack(track, trackids) :
Unknown track: UCSC Genes
The codes:
Library(GenomicFeatures)
mm8KG <- makeTranscriptDbFromUCSC(genome="mm8", tablename="knownGene")
sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets
methods base
other attached packages:
[1] GenomicFeatures_1.14.0 AnnotationDbi_1.24.0 Biobase_2.22.0
rtracklayer_1.22.0 GenomicRanges_1.14.3 XVector_0.2.0
IRanges_1.20.5
[8] BiocGenerics_0.8.0
loaded via a namespace (and not attached):
[1] biomaRt_2.18.0 Biostrings_2.30.0 bitops_1.0-6
BSgenome_1.30.0 DBI_0.2-7 RCurl_1.95-4.1 Rsamtools_1.14.1
RSQLite_0.11.4 stats4_3.0.2
[10] tools_3.0.2 XML_3.95-0.2 zlibbioc_1.8.0
Yours sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
[[alternative HTML version deleted]]