[BioC] Bug in getOntoly-function (package annotate)?

Marc Carlson mcarlson at fhcrc.org
Thu Oct 2 18:59:45 CEST 2008


Hi Jukka,

Can you please give us the results of calling sessionInfo()?  From what
I can see below it looks like you are using a custom annotation
package.  Is that correct?

  Marc


 

Jukka Hiissa wrote:
> Dear BioC users,
>
> I am having problems with the getOntology-function (annotate-package v.
> 1.18 ) The command
>
> getOntology(getGO( "7650504", "illuminaHumanBCv2")[[1]], "BP" )
> [1] "GO:0032515" "GO:0032516"
>
> returns two GO identifiers, but they are not correct since their
> ontologies are in fact NA
>
> $`GO:0032515`
> $`GO:0032515`$GOID
> [1] "GO:0032515"
> $`GO:0032515`$Evidence
> [1] "IDA"
> $`GO:0032515`$Ontology
> [1] NA
>
> $`GO:0032516`
> $`GO:0032516`$GOID
> [1] "GO:0032516"
> $`GO:0032516`$Evidence
> [1] "IDA"
> $`GO:0032516`$Ontology
> [1] NA
>
> I looked at the getOntology source code and I think that the problem is
> that the NAs are removed from the index vector but not from the list
> containing the GO-elements. The last two lines in the getOntology
> function are
>
> onts = onts[!is.na(onts)]
> unique(names(inlist[onts %in% which]))
>
> where the onts contains the ontology labels, e.g.
>
> GO:0000159 GO:0005524 GO:0005625 GO:0008160 GO:0008601 GO:0008601
>         NA       "MF"       "CC"       "MF"       "MF"       "MF"
> GO:0016887 GO:0019211 GO:0032515 GO:0032516 GO:0035307 GO:0035308
>       "MF"       "MF"         NA         NA       "BP"       "BP"
> GO:0042803 GO:0046982 GO:0051721
>       "MF"       "MF"       "MF"
>
> After the NAs are removed from the onts vector the indexes of the two
> BP-ontology cases are 8 and 9, but these are not the correct indexes for
> the inlist list, which still contains the three missing ontology cases.
>
> names( inlist )
> [1] "GO:0000159" "GO:0005524" "GO:0005625" "GO:0008160" "GO:0008601"
> [6] "GO:0008601" "GO:0016887" "GO:0019211" "GO:0032515" "GO:0032516"
> [11] "GO:0035307" "GO:0035308" "GO:0042803" "GO:0046982" "GO:0051721
>
> Best regards,
> Jukka Hiissa
>
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