[R] Bioconductor / AnnotationDbi: Why does a GOAllFrame contain more rows than its argument GoFrame?

[Martin Morgan]

On 10/02/2013 09:28 AM, Asis Hallab wrote:
> Dear Bioconductor Experts,

This will be responded to on the Bioconductor mailing list; please address any 
follow-ups there.

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Martin


>
> thank you for providing such a useful tool-set.
>
> I have a question regarding the package AnnotationDbi, specifically
> the classes GOFrame and GOALLFrame.
>
> During a GO Enrichment Analysis I create a data frame with Arabidopsis
> thaliana GO annotations and from that first a GOFrame and than from
> this GOFrame a GOALLFrame. Checking the result with
>
> nrow(  getGOFrameData(  athal.go.all.frame ) ) # The GOAllFrame
>
> and comparing it with
>
> nrow( athal.go.frame )                                     # The GoFrame
>
> I realize that the GOALLFrame has more than 5 times more rows than my
> original GO annotation table. If I provide
> organism='Arabidopsis thaliana'
> to the constructor of GOFrame this ratio increases even further.
>
> Unfortunately I could not find any documentation on this, so I feel
> forced to bother you with my questions:
>
> 1) Why does GOALLFrame so many more annotations?
> 2) Why and from where does it retrieve the organism specific ones that
> are added when a model organism like 'Arabidopsis thaliana' is
> provided?
> 3) I suspected that all ancestors of annotated terms are added, but
> when I did so myself, I still got less GO term annotations? So do you
> add ancestors of the "is_a" type and possibly other relationship types
> like "part_of" etc. ?
>
> Please let me know your answers soon. Your help will be much appreciated.
>
> Kind regards!
>
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