On 10/02/2013 09:28 AM, Asis Hallab wrote:
Dear Bioconductor Experts,
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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@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 ______________________________________________ R-help@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.
