[BioC] makeTranscriptDbFromBiomart - chrominfo failure
Marc Carlson
mcarlson at fhcrc.org
Sat Mar 16 01:22:21 CET 2013
Hi Stefanie,
This is not an error but a warning. It means that the data resource you
are extracting from does not indicate which chromosomes are
circular/linear or how long the various chromosomes are. You have to
decide if that matters to you or not. If it matters, then you might
want to see the manual page for seqlengths() and isCircular() and
consider settting that information manually.
Marc
On 03/15/2013 03:54 AM, Stefanie Tauber wrote:
> 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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