gseabase: infrastructure for gene-set associations

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

>>> import bioc.gseabase

XML description can be downloaded from the Broad Institute (http://www.broad.mit.edu/gsea/downloads.jsp)

>>> import from
>>> bioc.gseabase.__rpackage__.getBroadSets("")

The class inheritance diagram is useful for having an overview of how (biological) strings are modelled.

A module to model the GSEABase library in Bioconductor

Copyright 2009 - Laurent Gautier

class bioc.gseabase.GeneColorSet

coloring

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

genecolor

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

phenotype()

phenotypecolor()

rx(i)

class bioc.gseabase.GeneSet

collectiontype

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

contributor

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

creationdate

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

description

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

difference(gs)

geneids

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

geneidtype

maps GSEABase::geneIdType

intersection(gs)

longdescription

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

name

maps GSEABase::setName

organism

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

pubmedids

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

rx(i)

union(gs)

urls

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

class bioc.gseabase.GeneSetCollection(o)

geneids

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

names

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

bioc.gseabase.gseabase_conversion(robj)