[Bioc-devel] How to replace KEGG.db

[Vincent Carey]

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.Lottaz using 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
>
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