I did a little work in this area, relieving GenomicRanges of dependency on KEGG.db.
For your example, which does not run (?), I would suggest a) avoiding the use of the old environments like hgu95av2PATH2PROBE, replacing this with AnnotationDbi::select calls b) replace the KEGG.db invocations with KEGGREST equivalents. As an example, using AnnotationDbi, hgu95av2.db, and KEGGREST > select(hgu95av2.db, "JUNB", keytype="SYMBOL", columns=c("PROBEID", "PATH")) 'select()' returned 1:many mapping between keys and columns SYMBOL PROBEID PATH 1 JUNB 2049_s_at 04380 2 JUNB 32786_at 04380 > keggFind("pathway", "04380") path:map04380 "Osteoclast differentiation" On Mon, Feb 1, 2021 at 11:27 AM Claudio Lottaz < claudio.lot...@klinik.uni-regensburg.de> wrote: > Hi all, > > In my package adSplit, I use microarray annotation packages like > hgu95av2.db to find probes for pathways (in hgu95av2PATH2PROBE). In order > to find names out of these KEGG identifiers, I use KEGG.db. However, > KEGG.db is deprecated starting bioconductor 3.13 and bioconductor officials > suggest to use KEGGREST instead. Unfortunatly, KEGGREST seems not to find > information from these microarray annotation package IDs. E.g.: > > library(hgu95av2.db) > library(KEGG.db) > library(KEGGREST) > > path.id <- ls(hgu95av2PATH2PROBE)[1] > kegg.name <- KEGGPATHID2NAME[[path.id]] > print(kegg.name) > > keggrest.info <- keggGet(path.id) > print(keggrest.info) > > Does anybody have an idea, how to solve this? > > Cheers and thanks, > Claudio > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel