[BioC] filtering in GSEABase package

[James F. Reid]

Hi Jason,

the help page of GeneSetCollection specifies that using 'ontology' does 
work like 'evidence' where filtering is taking place.
You could filter out your results using GOTERM (GO.db) in this way:

goId %in% names(gg[lapply(mget(names(gg), GOTERM), Ontology) == "MF"])
##[1] TRUE
goId %in% names(gg[lapply(mget(names(gg), GOTERM), Ontology) == "BP"])


HTH,
J.


On 29/03/2010 18:41, Jason Lu wrote:
> Hi All,
>
> I noticed a problem which I am not sure if I miss something.
>
> I attempt to select GO terms in the biological process categories
> (BP). But for some reasons the filtering seems not working. One id is
> in the MF category, but still is selected (see below).
>
>
>   library(GSEABase)
>   data(sample.ExpressionSet)
>   gg<- GeneSetCollection(sample.ExpressionSet[200:250],
>                                        setType = GOCollection(ontology="BP"))
>
> goId = "GO:0003676"  # is in MF, not in BP
>
> goId %in% names(gg)
> TRUE
>
>> sessionInfo()
> R version 2.10.0 (2009-10-26)
> x86_64-redhat-linux-gnu
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] hgu95av2.db_2.3.5   org.Hs.eg.db_2.3.6  KEGG.db_2.3.5
>   [4] Category_2.12.0     GO.db_2.3.5         GSEABase_1.8.0
>   [7] graph_1.24.1        annotate_1.24.0     mouse4302.db_2.3.5
> [10] org.Mm.eg.db_2.3.6  RSQLite_0.7-3       DBI_0.2-5
> [13] AnnotationDbi_1.8.1 genefilter_1.28.2   ALL_1.4.7
> [16] Biobase_2.6.1
>
> loaded via a namespace (and not attached):
> [1] RBGL_1.22.0     splines_2.10.0  survival_2.35-7 tools_2.10.0
> [5] XML_2.6-0       xtable_1.5-6
>>
>
> Thanks for looking into this.
>
> Jason
>
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