[BioC] GRangesForUCSCGenome seems to be missing in rtracklayer 1.10, GenomicRanges 1.2

[Paul Shannon]

Hi Vince,

Yes, I suspected that right away.  Long function name, clumsy fingers, ...

Function name completion (I use ESS) and repeated typing led me to the same result.   

Just now I cut-and-pasted from your email into my R session

> GRangesForUCSCGenome
Error: object 'GRangesForUCSCGenome' not found

Puzzled,

 - Paul

On Oct 23, 2010, at 4:28 AM, Vincent Carey wrote:

> Perhaps you made a spelling error (though not in the email AFAICT)
> 
>> GRangesForUCSCGenome
> function (genome, chrom = NULL, ranges = NULL, ...)
> {
>    if (missing(genome) || !IRanges:::isSingleString(genome))
>        stop("'genome' must be a single string identifying a genome")
>    session <- browserSession("UCSC")
>    genome(session) <- genome
>    GRangesForGenome(genome, seqlengths(session), chrom = chrom,
>        ranges = ranges, ...)
> }
> <environment: namespace:rtracklayer>
>> sessionInfo()
> R version 2.12.0 Patched (2010-10-15 r53331)
> Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit)
> 
> locale:
> [1] C
> 
> attached base packages:
> [1] stats     graphics  grDevices datasets  tools     utils     methods
> [8] base
> 
> other attached packages:
> [1] rtracklayer_1.10.0 RCurl_1.4-3        bitops_1.0-4.1     weaver_1.15.0
> [5] codetools_0.2-2    digest_0.4.2
> 
> loaded via a namespace (and not attached):
> [1] BSgenome_1.18.0     Biobase_2.10.0      Biostrings_2.18.0
> [4] GenomicRanges_1.2.0 IRanges_1.7.40      XML_3.2-0
> 
> 
> On Sat, Oct 23, 2010 at 12:02 AM, Paul Shannon
> <pshannon at systemsbiology.org> wrote:
>> The rtracklayer vignette  features the GRangesForUCSCGenome rather prominently (page 3), but I cannot seem to find the function.
>> 
>> I can probably make do with 'GRanges', but my failure to match the vignette leaves me uneasy.
>> 
>> Any advice?    SessionInfo follows.
>> 
>>  - Paul
>> 
>>> sessionInfo ()
>> R version 2.12.0 (2010-10-15)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>> 
>> locale:
>> [1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8
>> 
>> attached base packages:
>> [1] tools     stats     graphics  grDevices utils     datasets  methods   base
>> 
>> other attached packages:
>>  [1] GenomicFeatures_1.1.11             rtracklayer_1.10.0                 RCurl_1.4-2                        bitops_1.0-4.1
>>  [5] BSgenome.Hsapiens.UCSC.hg18_1.3.16 BSgenome.Mmusculus.UCSC.mm9_1.3.16 BSgenome_1.17.5                    Biostrings_2.18.0
>>  [9] GenomicRanges_1.2.0                IRanges_1.8.0                      org.Pt.eg.db_2.4.1                 org.Hs.eg.db_2.4.6
>> [13] org.Mm.eg.db_2.4.1                 RSQLite_0.9-2                      DBI_0.2-5                          AnnotationDbi_1.11.8
>> [17] Biobase_2.10.0                     RUnit_0.4.25
>> 
>> loaded via a namespace (and not attached):
>> [1] biomaRt_2.6.0 XML_3.1-1
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