Question: adding KEGG annotations with ABPkBuilder from E.coli
gravatar for Marc Carlson
10.9 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Robert, I have just merged a patch into place for this. You should be able to get a new version of both the annotate and Category packages soon which should resolve this. Please let me know if there are any other issues. Marc Robert Castelo wrote: > hi all, > > i'm trying to build an annotation package for the Ecoli_ASv2 affy chip > and one of the things that i have not succeed to obtain is to > incorporate the available pathway annotations from KEGG. > > the problem seems to be within the function ABPkBuilder (from the > AnnBuilder package), when it calls 'getAnnData' and this functions does > the following line of code: > > pathNEnzyme <- try(mapLL2ECNPName(srcObjs[["kegg"]])) > > which runs smoothly without any problem but the resulting object called > pathNEnzyme is not using EntrezGeneIDs but the so-called Blattner IDs, > which are commonly used to refer to E.coli genes, and this must arise > from how KEGG stores pathway information for E.coli. > > I guess this is what afterwards bans the process of succeeding because > it tries to join these Blattner IDs (using the R function merge) with > the rest of the annotations based on EntrezGeneIDs. > > I can easily map Blattner IDs with EntrezGeneIDs but I don't know how to > tell ABPkBuilder to use these two sources of IDs to build the annotation > package, any idea? > > > thanks!! > robert. > ps: here goes my sessionInfo(): > R version 2.6.0 (2007-10-03) > x86_64-unknown-linux-gnu > > locale: > C > > attached base packages: > [1] tools stats graphics grDevices utils datasets > methods > [8] base > > other attached packages: > [1] GO_2.0.1 AnnBuilder_1.16.0 annotate_1.16.1 > [4] xtable_1.5-2 AnnotationDbi_1.0.6 RSQLite_0.6-4 > [7] DBI_0.2-4 XML_1.93-2 Biobase_1.16.1 > > loaded via a namespace (and not attached): > [1] rcompgen_0.1-15 > >
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