[BioC] Missing function locuslinkQuery and locuslinkBYID in annotate 1.18.0

[McGee, Monnie]

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
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor