Python Programming/Extending with R
It is possible to call R functions and even modules direcly from Python. One easy way to do this is the rpy2 interface. In the following code snippet, an R module called preprocessCore from the bioconductor portal is loaded and the quantile normalization function is applied on a matrix that is created in python and then converted back to python again.
importrpy2.robjectsasrobjectsfromrpy2.robjects.packagesimportimportrimportnumpypreprocessCore=importr('preprocessCore')matrix=[[1,2,3,4,5],[1,3,5,7,9],[2,4,6,8,10]]v=robjects.FloatVector([elementforcolinmatrixforelementincol])m=robjects.r['matrix'](v,ncol=len(matrix),byrow=False)Rnormalized_matrix=preprocessCore.normalize_quantiles(m)normalized_matrix=numpy.array(Rnormalized_matrix)It is thus possible to handle R modules and objects.
