[BioC] makeTranscriptDbFromBiomart - chrominfo failure
Stefanie Tauber
stefanie.tauber at univie.ac.at
Fri Mar 15 11:54:29 CET 2013
Hi,
I get the following warning:
library(GenomicFeatures)
myDB <- makeTranscriptDbFromBiomart(biomart = "ensembl", dataset =
"scerevisiae_gene_ensembl", circ_seqs = c(DEFAULT_CIRC_SEQS, "Mito"))
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... FAILED! (=> skipped)
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TranscriptDb object ... OK
Warning message:
In .normargChrominfo(chrominfo, transcripts$tx_chrom, splicings$exon_chrom) :
chromosome lengths and circularity flags are not available for this
TranscriptDb object
> sessionInfo()
R Under development (unstable) (2013-02-27 r62087)
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_1.11.16 AnnotationDbi_1.21.14 Biobase_2.19.3
[4] GenomicRanges_1.11.37 IRanges_1.17.37 BiocGenerics_0.5.6
loaded via a namespace (and not attached):
[1] biomaRt_2.15.1 Biostrings_2.27.11 bitops_1.0-5
[4] BSgenome_1.27.1 DBI_0.2-5 RCurl_1.95-4.1
[7] Rsamtools_1.11.22 RSQLite_0.11.2 rtracklayer_1.19.10
[10] stats4_3.0.0 tools_3.0.0 XML_3.95-0.2
[13] zlibbioc_1.5.0
Is this an issue of GenomicFeatures or Ensembl?
Best,
Stefanie
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