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

Jeff Newmiller jdnewmil at dcn.davis.CA.us
Wed Oct 2 19:24:06 CEST 2013

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Asis Hallab <asis.hallab at gmail.com> wrote:
>Dear Bioconductor Experts,
>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
>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
>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
>Kind regards!
>R-help at r-project.org mailing list
>PLEASE do read the posting guide
>and provide commented, minimal, self-contained, reproducible code.

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