Question: adding KEGG annotations with ABPkBuilder from E.coli
0
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 > >
ADD COMMENTlink written 10.9 years ago by Marc Carlson7.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour