CODEWITHSUNDEEP
rpackagebioconductorgenetics
Jacob Ritchie
Jacob Ritchie

Reputation: 1401

GO.db - Get newest Gene Ontology annotations

I am using the GO.db package in R (v3.3.2) to access information about the Gene Ontology. I can see by running the GO.db command that my annotations are outdated. (I know there are a newer set of annotations released in 2017).

> GO.db
GODb object:
| GOSOURCENAME: Gene Ontology
| GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
| GOSOURCEDATE: 2016-Sep21
| Db type: GODb
| package: AnnotationDbi
| DBSCHEMA: GO_DB
| GOEGSOURCEDATE: 2016-Sep26
| GOEGSOURCENAME: Entrez Gene
| GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
| DBSCHEMAVERSION: 2.1

I've tried uninstalling and reinstalling the package, but the GOSOURCEDATE value remains unchanged.

I want to find out what sequence of R commands will allow me to load the newer annotations. Do I need to install a newer version of R?

The Bioconductor version information is as follows:

> BiocInstaller::biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).

The output of the sessionInfo command is as follows (includes a lot of unrelated packages that my application also loads.

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252    LC_MONETARY=English_Canada.1252
[4] LC_NUMERIC=C                    LC_TIME=English_Canada.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] cowplot_0.8.0        ggplot2_2.2.1        xlsx_0.5.7           xlsxjars_0.6.1       rJava_0.9-8         
 [6] reshape2_1.4.2       metap_0.8            GO.db_3.4.0          annotate_1.52.1      XML_3.98-1.9        
[11] org.Hs.eg.db_3.4.0   AnnotationDbi_1.36.2 IRanges_2.8.2        S4Vectors_0.12.2     Biobase_2.34.0      
[16] BiocGenerics_0.20.0  homologene_1.0       magrittr_1.5         tidyr_0.7.1          dplyr_0.7.3         
[21] readr_1.1.1          tmod_0.31           

loaded via a namespace (and not attached):
 [1] beeswarm_0.2.3     purrr_0.2.3        lattice_0.20-34    colorspace_1.3-2   htmltools_0.3.6    blob_1.1.0        
 [7] rlang_0.1.2        glue_1.1.1         DBI_0.7            bit64_0.9-7        RColorBrewer_1.1-2 bindrcpp_0.2      
[13] bindr_0.1          plyr_1.8.4         pca3d_0.10         stringr_1.2.0      munsell_0.4.3      gtable_0.2.0      
[19] htmlwidgets_0.9    memoise_1.1.0      knitr_1.17         httpuv_1.3.5       Rcpp_0.12.12       xtable_1.8-2      
[25] scales_0.5.0       jsonlite_1.5       mime_0.5           bit_1.1-12         ellipse_0.3-8      hms_0.3           
[31] digest_0.6.12      stringi_1.1.5      tagcloud_0.6       shiny_1.0.5        grid_3.3.2         tools_3.3.2       
[37] bitops_1.0-6       rgl_0.98.1         lazyeval_0.2.0     RCurl_1.95-4.8     tibble_1.3.4       RSQLite_2.0       
[43] pkgconfig_2.0.1    assertthat_0.2.0   R6_2.2.2           plotwidgets_0.4

Upvotes: 0

Views: 643

Answers (1)

dvantwisk
dvantwisk

Reputation: 561

I couldn't find your question on the support site, so I can give you one here.

It seems that you are using Bioconductor version 3.4. It appears that all of your annotation packages are out-of-date. If you want to use the current release annotations, you will have to update your version of R to the current release version (3.4.1) and then run the command BiocInstaller::biocLite("biocUpgrade").

Upvotes: 1

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