[BioC] Missing function locuslinkQuery and locuslinkBYID in annotate 1.18.0

[Marc Carlson]

Hi Monnie,

You will need to run the 1.19.3 version of the annotate package. 

http://www.bioconductor.org/packages/2.3/bioc/html/annotate.html


  Marc



McGee, Monnie wrote:
> Dear Mark,
>
> Thank you.
>
> I don't have access to the source tree.  Does this mean that I need to download the annotate library again, or can I grab the functions separately?   If the latter, how is that done?
>
> Best,
> Monnie
>
> Monnie McGee, Ph.D.
> Associate Professor
> Department of Statistical Science
> Southern Methodist University
> Ph: 214-768-2462
> Fax: 214-768-4035
>
>
>
> -----Original Message-----
> From: Marc Carlson [mailto:mcarlson at fhcrc.org]
> Sent: Wed 10/8/2008 11:03 AM
> To: McGee, Monnie
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Missing function locuslinkQuery and locuslinkBYID in	annotate 1.18.0
>  
> Hi Monnie,
>
> These functions seem to have disappeared as we moved from the older
> annotations to the new kind.  I have just checked in some replacement
> functions for you into the development branch (entrezGeneByID() and
> entrezGeneQuery()).  If you have access to the source tree then these
> are already available, but they should be on the website within 24 hours.
>
>   Marc
>
>
>
> McGee, Monnie wrote:
>   
>> Dear List,
>>
>> I was going through the examples in the query documentation (written in June of 2008) for the annotate package when I came to an error.   The function "locuslinkQuery" no longer seems to exist, and neither does "locuslinkByID".    Here are my code and session info:
>>
>>   
>>     
>>> sessionInfo()
>>>     
>>>       
>> R version 2.7.2 (2008-08-25) 
>> powerpc-apple-darwin8.11.1 
>>
>> locale:
>> C
>>
>> attached base packages:
>> [1] splines   tools     stats     graphics  grDevices
>> [6] utils     datasets  methods   base     
>>
>> other attached packages:
>>  [1] XML_1.96-0          cMAP_1.15.1        
>>  [3] GOstats_2.6.0       Category_2.6.0     
>>  [5] genefilter_1.20.0   survival_2.34-1    
>>  [7] RBGL_1.16.0         annotate_1.18.0    
>>  [9] xtable_1.5-3        GO.db_2.2.0        
>> [11] hgu133a_2.2.0       RbcBook1_1.8.0     
>> [13] graph_1.18.1        KEGG_2.2.0         
>> [15] hgu95av2.db_2.2.0   AnnotationDbi_1.2.1
>> [17] RSQLite_0.6-8       DBI_0.2-4          
>> [19] Biobase_2.0.1       hgu95av2_2.2.0     
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.11.11
>>
>>   
>>     
>>> locuslinkQuery("leukemia","Hs")
>>>     
>>>       
>> Error: could not find function "locuslinkQuery"
>>
>> The annotate package is attached, as are BioBase and XML, which are the packages that the documentation states are needed.  I noticed that the session info for the documenation had XML version 1.95.2 instead of 1.96-0 as in mine.   I also listed all of the functions available in the annotate package, using ls(package:annotate) and locuslinkQuery is not there.  I looked around for various substitutes, but I could not find any.   Has this function been removed?  If so, what is its replacement?  If not, what did I do wrong?
>>
>> I also searched the help archives, but did not find any reference to this problem.
>>
>> By the way, right now I have to set my locale to "C"  every time I start R.  Is there a way to make this automatic?
>>
>> Thanks,
>> Monnie
>>
>> Monnie McGee, Ph.D.
>> Associate Professor
>> Department of Statistical Science
>> Southern Methodist University
>> Ph: 214-768-2462
>> Fax: 214-768-4035
>>   
>> ------------------------------------------------------------------------
>>
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>>     
>
>
>
>