[BioC] Genominator problem

[Kasper Daniel Hansen]

Inside the function, annoData is just the yAnno data.frame.

The error means that transcript.id - with a default value of
"ensembl_transcript_id" is not part of the names (colnames) of the
yAnno object.

At this time you should show us
  head(yAnno)
and tell us exactly what document you are following.

Kasper

On Fri, Aug 27, 2010 at 10:03 AM, Johnny H <ukfriend22 at googlemail.com> wrote:
> Thanks Kasper for that, the command works but...
>
>> yAnnoUI <- makeGeneRepresentation(yAnno, type = "UIgene")
> Error: transcript.id %in% names(annoData) is not TRUE
>> annoData
> Error: object 'annoData' not found
> Where is annoData coming from?
>
> On Fri, Aug 27, 2010 at 2:59 PM, Kasper Daniel Hansen
> <kasperdanielhansen at gmail.com> wrote:
>>
>> This function has been replaced by the more general
>> makeGeneRepresentation.  So the call would now be
>>
>> yAnnoUI <- makeGeneRepresentation(yAnno, type = "UIgene")
>>
>> (there are arguments that allow you to set the gene.id and
>> transcript.id but the defaults are set as below).
>>
>> Kasper
>>
>> On Fri, Aug 27, 2010 at 9:48 AM, Johnny H <ukfriend22 at googlemail.com>
>> wrote:
>> > Dear Bioconductors,
>> > I am using the Genominator library and work through the example...until
>> > I
>> > get to here
>> >
>> >> yAnnoUI <- Genominator:::makeUIgenes(yAnno, gene.id =
>> >> "ensembl_gene_id",
>> > transcript.id = "ensembl_transcript_id", verbose = TRUE)
>> > Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
>> >  object 'makeUIgenes' not found
>> >
>> > Please can you advise me how I can use the makeUIgenes method?
>> > Subsequent
>> > steps in the example don't work without this step.
>> >
>> > Thank you.
>> >
>> >> sessionInfo()
>> > R version 2.11.1 (2010-05-31)
>> > i386-pc-mingw32
>> > locale:
>> > [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
>> > Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
>> > LC_NUMERIC=C                            LC_TIME=English_United
>> > Kingdom.1252
>> > attached base packages:
>> > [1] grid      stats     graphics  grDevices utils     datasets  methods
>> > base
>> > other attached packages:
>> >  [1] rtracklayer_1.8.1   RCurl_1.4-3         bitops_1.0-4.1
>> > Genominator_1.2.0   GenomeGraphs_1.8.0  biomaRt_2.4.0
>> > RSQLite_0.9-2       DBI_0.2-5           ShortRead_1.6.2
>> > Rsamtools_1.0.8     lattice_0.18-8
>> > [12] Biostrings_2.16.9   GenomicRanges_1.0.8 IRanges_1.6.15
>> > yeastRNASeq_0.0.3
>> > loaded via a namespace (and not attached):
>> > [1] Biobase_2.8.0   BSgenome_1.16.5 hwriter_1.2     tools_2.11.1
>> > XML_3.1-1
>> >
>> >        [[alternative HTML version deleted]]
>> >
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>
>