Marc Carlson | 16 Mar 01:22 2013

Re: makeTranscriptDbFromBiomart - chrominfo failure

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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