[BioC] Genominator problem

[Kasper Daniel Hansen]

This function has been replaced by the more general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
>
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