annotationdbi: base structures and functions for annotations

The module reflects the content of the R/Bioconductor package AnnnotationDbi. It defines Python-level classes for the R/S4 classes, and gives otherwise access to R-level commands the usual rpy2:robjects way.

The variable annotationdbi_env in the module is an rpy2.robjects.REnvironment for the modules namespace. Accessing explicitly a module’s object is then straightforward.

The class inheritance diagram presents the parent-child relationships between the elements.

Inheritance diagram of bioc.annotationdbi

class bioc.annotationdbi.AnnDbBimap
get_lkeys()
get_rkeys()
lkeys
mappedlkeys()
mappedrkeys()
rkeys
set_lkeys(value)
set_rkeys(value)
subset(lkeys=None, rkeys=None, objname=None)
class bioc.annotationdbi.AnnDbMap
class bioc.annotationdbi.Bimap

A Bimap as defined in the R package AnnotationDbi

count_mappedkeys()
keys()
mappedkeys()
subset(lkeys=None, rkeys=None)
class bioc.annotationdbi.GOTerms
GOID
maps AnnotationDbi::GOID
definition
maps AnnotationDbi::Definition
ontology
maps AnnotationDbi::Ontology
secondary
maps AnnotationDbi::Secondary
synonym
maps AnnotationDbi::Synonym
term
maps AnnotationDbi::Term
bioc.annotationdbi.annotationdbi_conversion(robj)

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