Missing function locuslinkQuery and locuslinkBYID in annotate 1.18.0
1
0
Entering edit mode
McGee, Monnie ▴ 300
@mcgee-monnie-1108
Last seen 7.4 years ago
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
GO hgu95av2 Biobase annotate GO hgu95av2 Biobase annotate • 596 views
ADD COMMENT
0
Entering edit mode
Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.5 years ago
United States
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
ADD COMMENT

Login before adding your answer.

Traffic: 489 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6