Introduction

Installing bioconductor packages

Installing bioconductor packages can easily be done through the biocLite function, that fetches and install packages over the internet. That procedure can be used from rpy2:

import rpy2.robjects as robjects
from rpy2.robjects.packages import importr
base = importr('base')

# evaluate locally a remote R script
base.source("http://www.bioconductor.org/biocLite.R")
bioclite = robjects.globalenv['biocLite']

# download and install a bioconductor package
bioclite("<name of the bioconductor package>")

Module structures

Each modules in the package is representing a bioconductor package, and all modules have the following characteristics:

• the module name is all lower-case (while the corresponding R package name can be mix of a upper and lower case).
• the corresponding R package is loaded (silently) when the module is imported
• Python classes, and eventually functions, representing the R classes (and eventually functions) are defined
• the module variable __rname__ contains the name of the corresponding R package
• the module variable __rpackage__ represent the full R package