[R] Bioconductor / AnnotationDbi: Why does a GOAllFrame contain more rows than its argument GoFrame?
asis.hallab at gmail.com
Wed Oct 2 18:28:36 CEST 2013
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
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 appreciated.
More information about the R-help