I 'upgraded' my BioC installation today, including the annotation packages, and also installed
reactome.db which I would like to use for pathway analyses of a dataset in the near future. However, I am confused on whether the content of
reactome.db is still up to date. I am asking because I cannot really find which version of Reactome is packaged.
I assumed it would be the latest version (i.e. V58 [released September 28 2016], or maybe V57 [from June 27 2016]). However, when I check the help pages from
reactome.db, I noticed that the time stamp for all annotation objects (e.g. reactomeEXTID2PATHID) is 2010-Dec-21(= ~6 yrs ago...). On the other end, in the description file it is mentioned that it was packed on 2016-04-14, which rather suggests the content is based on the V56 release [from March 24 2016]...
I also noticed on the list that there were some problems with
reactome.db that prevented the incorporation of new data, but it was suggested these were solved ~2 years ago (see this thread from the archive: reactome.db is not updated?).
Anyway, I am lost, so any insights on this (or alternatives) would be appreciated.
<<edit>> Added sessionInfo()
<<edit2>> also found this informative thread: A: Reactome pathway names from IDs?.
> sessionInfo() R version 3.3.1 Patched (2016-10-18 r71535) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale:  LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252 LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  parallel stats4 stats graphics grDevices utils datasets methods  base other attached packages:  reactome.db_1.55.0 AnnotationDbi_1.36.0 IRanges_2.8.0 S4Vectors_0.12.0  Biobase_2.34.0 BiocGenerics_0.20.0 BiocInstaller_1.24.0 loaded via a namespace (and not attached):  DBI_0.5-1 tools_3.3.1 RSQLite_1.0.0 >