Asis Hallab
2013-Oct-02 16:28 UTC
[R] Bioconductor / AnnotationDbi: Why does a GOAllFrame contain more rows than its argument GoFrame?
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 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!
Jeff Newmiller
2013-Oct-02 17:24 UTC
[R] Bioconductor / AnnotationDbi: Why does a GOAllFrame contain more rows than its argument GoFrame?
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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
>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!
>
>______________________________________________
>R-help at r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
Martin Morgan
2013-Oct-02 17:32 UTC
[R] Bioconductor / AnnotationDbi: Why does a GOAllFrame contain more rows than its argument GoFrame?
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. http://bioconductor.org/help/mailing-list/ 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! > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793