[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! __ 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.
Re: [R] Bioconductor / AnnotationDbi: Why does a GOAllFrame contain more rows than its argument GoFrame?
You have addressed the wrong mailing list. See http://www.bioconductor.org/help/mailing-list/ --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Asis Hallab asis.hal...@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@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. __ 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.
Re: [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@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.
